Methods and compositions for modulating the innate immune response and/or myogenesis in a mammalian subject

ABSTRACT

In one aspect, the present invention relates to methods for increasing, decreasing or maintaining the innate immune response in a mammalian subject comprising modulating the expression of DUX4-fl, or modulating the expression of beta-defensin 3 (DEFB103). In another aspect, the present invention relates to methods for increasing, decreasing or maintaining myogenesis or muscle differentiation in a mammalian subject comprising modulating the expression of beta-defensin 3 (DEFB103). In additional aspects, the present invention involves diagnostic methods based on assessment of identified biomarkers.

This application claims priority to U.S. Application Nos. 61/513,456 and 61/453, 467 filed on Jul. 29, 2011, U.S. Application No. 61/556,099 filed on Nov. 4, 2011, the entire contents of which are hereby incorporated by reference without disclaimer.

This Invention was made with government support under NS069539, AR045113 and AR0045203 awarded by National Institutes of Health. The government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention relates generally to medicine, diagnostic and therapeutic methods. In particular, embodiments are directed to the diagnosis and treatment of DUX-4 related disorders, such as muscular dystrophy, autoimmune diseases, infection, and cancer.

BACKGROUND

Immunity can generally be classified as innate immunity or as adaptive immunity Innate immune responses typically occur immediately upon infection to provide an early barrier to infectious disease whereas adaptive immune responses occur later with the generation of antigen-specific effector cells and often long term protective immunity.

The innate immune system, also known as non-specific immune system and first line of defense, comprises the cells and mechanisms that defend the host from infection by other organisms in a non-specific manner. This means that the cells of the innate system recognise and respond to pathogens in a generic way, but unlike the adaptive immune system, it does not confer long-lasting or protective immunity to the host. Innate immune systems provide immediate defense against infection, and are found in all classes of plant and animal life. The innate immune system is thought to constitute an evolutionarily older defense strategy.

There remains a need to identify strategies to modulate immune activation, including control of unwanted activation of the innate immune response or increase desired innate immune response.

Facioscapulohumeral dystrophy (FSHD) is the third most common muscular dystrophy. The mutation that causes FSHD was identified nearly 20 years ago (Wijmenga et al., 1992), yet the molecular mechanism(s) of the disease remains elusive. The most prevalent form of FSHD (FSHD1) is caused by the deletion of a subset of D4Z4 macrosatellite repeats in the subtelomeric region of chromosome 4q. Unaffected individuals have 11-100 of the 3.3 kb D4Z4 repeat units, whereas FSHD1 individuals have 10 or fewer repeats. At least one repeat unit appears necessary for FSHD because no case has been identified with a complete deletion of D4Z4 repeats (Tuplet et al., 1996). Each repeat unit contains a copy of the double homeobox retrogene DUX4 (Clapp et al., 2007; Gabriels et al., 1999; Lyle et al., 1995), and inappropriate expression of DUX4 was initially proposed as a possible cause of FSHD. This was supported by the observations that repeat contraction is associated with decreased repressive epigenetic marks in the remaining D4Z4 units (van Overveld et al., 2003; Zeng et al., 2009), and that overexpression of the DUX4 protein in a variety of cells, including skeletal muscle, causes apoptotic cell death (Kowaljow et al., 2007; Wallace et al., 2011; Wuebbles et al., 2010). However, initial attempts to identify DUX4 mRNA transcripts in FSHD muscle were unsuccessful, leading to the suggestion that other genes in the region were causative for FSHD (Gabellini et al., 2002; Klooster et al., 2009; Laoudj-Chemvesse et al., 2005; Reed et al., 2007).

Currently, the diagnostic test for FSHD1 requires pulse-field gel electrophoresis and Southern blotting to detect the contraction of the D4Z4 repeats, and there are no commercially available diagnostic tests for FSHD2.

SUMMARY OF THE INVENTION

In accordance with the foregoing, in one aspect, the invention provides a method of inhibiting the innate immune response in a mammalian subject in need thereof, comprising administering to the mammalian subject an agent capable of inducing, or increasing the level of DUX4-fl expression in a population of cells in the mammalian subject.

In another aspect, the invention provides a method of inhibiting the innate immune response in a mammalian subject in need thereof, comprising administering to the mammalian subject an agent capable of inducing, or increasing the level of DEFB103A and/or DEFB103B expression in a population of cells in the mammalian subject.

In another aspect, the invention provides a method of increasing or maintaining the innate immune response in a mammalian subject in need thereof, comprising administering to the mammalian subject an agent capable of inhibiting, or suppressing the level of DUX4-fl expression, or an agent capable of inhibiting DUX4-fl mediated transcription activation in a population of cells in the mammalian subject.

In another aspect, the invention provides a method of inducing one or more testis expressed genes in a non-testis cell type comprising contacting the non-testis cell type with an agent capable of inducing, or increasing the level of DUX4-fl expression in a population of cells.

In accordance with the foregoing, in one aspect, the invention provides a method of determining the presence of, or risk of developing, Facioscapulohumeral dystrophy (FSHD) in a mammalian subject. The method in accordance with this aspect comprises: (a) determining the presence or amount of at least one FSHD biomarker in a biological test sample obtained from a mammalian subject, wherein the at least one FSHD biomarker comprises a gene product of a DUX-4-fl induced gene; and (b) comparing the presence or amount of the biomarker determined in step (a) with a reference standard or control sample, wherein an increase in the presence or amount of the FSHD biomarker determined in the test sample in comparison to the reference standard or control sample is indicative of the presence of FSHD, or increased risk of developing FSHD, in the mammalian subject.

In another aspect, the invention provides an isolated polynucleotide probe for detecting an FSHD biomarker, or a polynucleotide primer for amplifying at least a portion of an FSHD biomarker, wherein the nucleic acid probe or primer has a length of from at least 10 nucleotides to 200 nucleotides (i.e., from 10-50, 50-100, nucleotides, or 15, 20, 50, 75, 100, 150, or 175 nucleotides in length) and specifically hybridizes to the nucleic acid sequence of at least one FSHD biomarker set forth in TABLE 1 or TABLE 2.

In another aspect, the invention provides an isolated population of polynucleotide probes comprising a plurality of polynucleotides each complementary and hybridizable to a sequence of at least two different FSHD biomarkers selected from any one of TABLE 1 or TABLE 2.

In another aspect, the invention provides an isolated antibody that specifically binds to an FSHD polypeptide biomarker encoded by a nucleic acid set forth in TABLE 1 or TABLE 2. In another aspect, the invention provides a kit comprising one or more detection reagents for detecting one or more FSHD biomarkers set forth in TABLE 1 or TABLE 2 for use in an assay to determine the presence or risk of FSHD in a biological sample obtained from a mammalian subject.

In another aspect, the invention provides a nucleic acid molecule comprising an expression cassette comprising a promoter operationally linked to a reporter gene or selectable marker, wherein the promoter contains at least one DUX4-responsive element comprising the consensus sequence “TAAYBBAATCA” (SEQ ID NO:166).

In another aspect, the invention provides a method of detecting the presence of DUX4-fl protein in a cell sample comprising introducing a nucleic acid molecule comprising an expression cassette comprising a promoter operationally linked to a reporter gene or selectable marker, wherein the promoter contains at least one DUX4-responsive element comprising the consensus sequence “TAAYBBAATCA” (SEQ ID NO:166), and assaying the cell for expression of the reporter gene, or selecting for growth under conditions requiring expression of the selectable marker.

In another aspect, the invention provides a method of identifying an inhibitor of DUX4-fl induced expression. The method in accordance with this aspect of the invention comprises: (a) contacting a cell containing (i) an expression cassette comprising a promoter operationally linked to a reporter gene or selectable marker, wherein the promoter contains at least one DUX4-responsive element comprising the consensus sequence “TAAYBBAATCA” (SEQ ID NO:166), and (ii) DUX4-fl polypeptide, with a candidate inhibitory agent; and (b) determining whether the cell expresses the reporter gene or selectable marker in the presence and absence of the candidate inhibitory agent, wherein the absence of expression of the reporter gene or selectable marker in the presence of the inhibitory agent indicates that the agent is an inhibitor of DUX4-fl induced expression.

In further embodiments, methods may also involve determining the presence or absence of a polymorphism resulting in a functional polyadenylation sequence operationally linked to exon 3 of the DUX4 gene. The determination may involve genotyping a biolodical sample. A determination of the absence of a functional polyadenylation sequence operationally linked to exon 3 may indicate the subject does not have a genetic predisposition to develop or is not suffering from FSHD, while the presence of the sequence may indicate a predisposition toward developing the disease (or the presence of the disease already). In certain embodiments, the polymorphism is described in PCT/US2011/048318, which has been published as WO/2012/024535, which is hereby incorporated by reference.

Embodiments discussed in the context of methods and/or compositions of the invention may be employed with respect to any other method or composition described herein. Thus, an embodiment pertaining to one method or composition may be applied to other methods and compositions of the invention as well.

As used herein the terms “encode” or “encoding” with reference to a nucleic acid are used to make the invention readily understandable by the skilled artisan; however, these terms may be used interchangeably with “comprise” or “comprising” respectively.

As used herein the specification, “a” or “an” may mean one or more. As used herein in the claim(s), when used in conjunction with the word “comprising”, the words “a” or “an” may mean one or more than one.

The use of the term “or” in the claims is used to mean “and/or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and/or.” As used herein “another” may mean at least a second or more.

Throughout this application, the term “about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects.

Other objects, features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating preferred embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.

DESCRIPTION OF THE DRAWINGS

The foregoing aspects and many of the attendant advantages of this invention will become more readily appreciated as the same become better understood by reference to the following detailed description, when taken in conjunction with the accompanying drawings, wherein:

FIG. 1 shows the results of RT-PCR validation of DUX-fl induced target genes shown to be upregulated in the expression microarray, (−) unstransfected cells; (+) transfected cells, as described in Example 1;

FIG. 2A illustrates the structure of the luciferase reporter construct containing a 31 bp DUX binding site (obtained from genomic regions of TRIM48 or ZCAN4 genes) located upstream of an SV40 promoter cloned into pGL3-promoter reporter vector, as described in Example 2;

FIG. 2B graphically illustrates the results of human rhabdomyoscaroma cell line RD transfected with the reporter construct containing the DUX4 binding site from TRIM48. Cells were co-transfected with the reporter construct and DUX4-fl or DUX4-s. pCS2-β galactosidase (beta gal) was used to balance DNA amount in control condition. TRIM48mut=construct containing a mutated binding site. Luciferase activity was set relative to control, as described in Example 2;

FIG. 2C graphically illustrates the results of human rhabdomyoscaroma cell line RD transfected with the reporter construct containing the DUX4 binding site from ZCAN4. Cells were co-transfected with the reporter construct and DUX4-fl or DUX4-s. pCS2-β galactosidase (beta gal) was used to balance DNA amount in control condition. ZSCAN4mut=construct containing a mutated binding site. Luciferase activity was set relative to control, as described in Example 2;

FIG. 2D shows the relative luciferase activity in the presence of DUX4-fl from a reporter construct in which the 31 bp DUX4 binding site was inserted in reverse orientation upstream of the SV40 promoter, as described in Example 2;

FIG. 2E shows the relative luciferase activity from a reporter construct in which the 31 bp DUX4 binding site was inserted in the original orientation, but moved downstream of the reporter gene, as described in Example 2;

FIG. 3 is a Heat map showing expression of cancer testis antigens (CTA) in HCT116 cells under conditions that activate DUX4-fl expression (i.e. treatment with the demethylating agent 5-azacytidine). The relative expression of the CTA in each row was measured by RT-PCR and represented as high (yellow, or light shading) or low (black, dark shading). The first column shows very low expression of CTAs in HCT116 that are not treated (−) and the second column shows a robust induction after treatment with azacytidine (+), a condition that induces expression of DUX4-fl, as described in Example 4;

FIG. 4 graphically illustrates that Pargyline decreases the amount of DUX4 mRNA in FSHD muscle cells. FSHD muscle cells that express endogenous DUX4-fl mRNA were treated with the MAO inhibitor Pargyline that has been reported to inhibit the histone demethylase LSD1, or with another MAO inhibitor tranylcypromine that has a different spectrum of activity on demethylase. The pargyline decreases the abundance of DUX4-fl mRNA in a dose dependent manner as measured by quantitative RT-PCR, as described in Example 6;

FIG. 5 graphically illustrates that Pargyline has a dose dependent inhibition of DUX4 mRNA expression in FSHD muscle cells. Cultured FSHD muscle cells were differentiated for 48 hours in differentiation medium (DM) with varying amounts of pargyline and the amount of DUX4-fl mRNA was measured by RT-PCR. There was a dose dependent inhibition of DUX4 expression (top panel). Middle panel is a no RT control and bottom panel is a GAPDH loading control, as described in Example 6;

FIG. 6 demonstrates that the protein synthesis inhibitor cycloheximide (chx) prevents decay of the DUX4 mRNA, as described in Example 6;

FIG. 7A graphically illustrates the expression levels (as determined by real-time PCR analysis of cultured myoblasts) of innate immune responder IFIH1 after infection with lenti-GFP or lenti-DUX4-fl, as described in Example 8;

FIG. 7B graphically illustrates the expression levels (as determined by real-time PCR analysis of cultured myoblasts) of secreted factor DEFB103 after infection with lenti-GFP or lenti-DUX4-fl, as described in Example 8;

FIG. 8A-8B graphically illustrates the expression levels (as determined by real-time PCR analysis of cultured myoblasts) of innate immune responders IFIH1 (FIG. 8A) and ISG20 (FIG. 8B) after infection with lenti-GFP in either media supplemented with human β-defensin 3 peptide or conditioned media (CM) from lenti-DUX4-fl, as described in Example 8;

FIG. 9 graphically illustrates the endogenous expression of DEFB103 in control testis and skeletal muscle tissues, FSHD muscle biopsies, and cultured FSHD and control muscle cells, as described in Example 8;

FIG. 10 graphically illustrates the upregulation of myostatin (MSTN) in β-defensin 3 peptide (DEFB103) treated myoblasts cultured in growth media, as described in Example 8;

FIG. 11A-11G graphically illustrates the expression levels of various muscle marker genes (FIG. 11A: ACTA1; FIG. 11B: CKM; FIG. 11C: CASQ2; FIG. 11D: MYH2; FIG. 11E: TNNT3; FIG. 11F: MYG6; and FIG. 11G: DESMIN) in response to human β-defensin when added to myoblasts cultured in differentiation media. MYG6 (FIG. 11F) and DESMIN (FIG. 11G) were included as genes that were unchanged on the arrays, as described in Example 8.

FIG. 12A-12B. UPF1 knock-down increases the abundance of the DUX4 mRNA and the expression of the DUX4 target gene ZSCAN4. A. Semiquantitative RT-PCR showing DUX4 expression in growth medium (GM) and differentiation medium (DM) from FSHD muscle cells. siUPF1 represents cells transfected with an si RNA to knock-down UPF1; siluc is the control si RNA to luciferase which is not expressed in the cells. DUX4 mRNA is detected in DM and is at higher levels in cells with the UPF1 knockdown. B. Determination by quantitative RT-qPCR of the levels of the DUX4 target gene ZSCAN4, as described in Example 9.

DETAILED DESCRIPTION

Unless specifically defined herein, all terms used herein have the same meaning as they would to one skilled in the art of the present invention.

As used herein the term “the innate immune response” refers to the cellular pathways that respond to pathogen associated molecular patterns and activate a defense response through the RIG-1-like receptors, the toll-like receptors, or other pathogen associated molecular pattern receptors to activate interferon, NF-kapa-B, STAT, IRF and other response pathways that protect against pathogen infection. Indicators of the activation of the innate immune response include increased expression and/or phosphorylation of IRF family members, increased expression of the RIG-I like receptors, and increased expression of interferons and/or chemokines.

The terms “percent identity” or “percent identical,” as applied to polypeptide sequences, such as the polypeptides encoded by the DUX4-fl induced genes set forth in TABLES 1 and 2, or a portion thereof, is defined as the percentage of amino acid residues in a candidate protein sequence that are identical with the subject protein sequence (such as the amino acid sequence encoded by SEQ ID NO:1, or a portion thereof comprising at least 10 consecutive amino acid residues) after aligning the candidate and subject sequences to achieve the maximum percent identity. For example, percentage identity between two protein sequences can be determined by pairwise comparison of the two sequences using the bl2seq interface at the Web site of the National Center for Biotechnology Information (NCBI), U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda, Md. 20894, U.S.A. The bl2seq interface permits sequence alignment using the BLAST tool described by Tatiana et al. (1999). The following alignment parameters are used: Matrix=BLOSUM62; Gap open penalty=11; Gap extension penalty=1; Gap x_dropff=50; Expect=10.0; Word size=3; and Filter=off. In some embodiments, the FSHD polypeptide biomarkers comprise at least 90%, or at least 95%, or at least 99% identity to the polypeptides encoded by the DUX4-fl induced genes set forth in TABLES 1 or 2, including naturally occurring variants thereof. The terms “percent identity” or “percent identical,” as applied to nucleic acid molecules, is the percentage of nucleotides in a candidate nucleic acid sequence that are identical with a subject nucleic acid molecule sequence (such as the nucleic acid molecule sequence set forth in SEQ ID NO:1, or a portion thereof comprising at least 20 consecutive nucleotides) after aligning the sequences to achieve the maximum percent identity, and not considering any nucleic acid residue substitutions as part of the sequence identity. No gaps are introduced into the candidate nucleic acid sequence in order to achieve the best alignment. Nucleic acid sequence identity can be determined in the following manner. The subject polynucleotide molecule sequence is used to search a nucleic acid sequence database, such as the Genbank database, using the program BLASTN version 2.1 (based on Altschul et al., 1997). The program is used in the ungapped mode. Default filtering is used to remove sequence homologies due to regions of low complexity as defined in Wootton and Federhen (1996). The default parameters of BLASTN are utilized. In some embodiments, the FSHD gene biomarkers comprise at least 90%, or at least 95%, or at least 99% identity to the nucleic acid sequences of the DUX4-fl induced genes set forth in TABLES 1 or 2, including naturally occurring variants thereof.

As used herein, the term “healthy human subject” refers to an individual who is known not to suffer from FSHD, such knowledge being derived from clinical data on the individual. As used herein, the term “DUX4-fl induced gene product” refers to a gene product (mRNA or polypeptide) expressed from a gene that is induced at least 2-fold (i.e. at least 3-fold, at least 5-fold, at least 8-fold, at least 10-fold, at least 16 fold or greater) in the presence of DUX4-fl, including genes driven by a promoter that is directly bound by DUX4-fl as well as genes that are induced indirectly by DUX4-fl. In some embodiments, the DUX4-fl induced genes contain one or more DUX4-fl responsive element(s) which are directly bound by DUX4-fl. As used herein, the term “DUX4-fl” encompasses naturally occurring DUX4-fl protein that is isolated from a human subject (i.e. SEQ ID NO:110, or a naturally occurring variant thereof, encoded by at least one of SEQ ID NO:108 or SEQ ID NO:109, or a naturally occurring variant thereof), as well as cultured cells making DUX4-fl, or made by recombinant DNA technology (e.g., in eukaryotic expression systems (e.g., COS cells)), in yeast, mammalian, or in bacterial expression systems). The term “variant of DUX4-fl” refers to a polypeptide comprising at least 90%, or at least 95%, or at least 99% identity to DUX4-fl polypeptide, set forth as SEQ ID NO:110, including naturally occurring variants thereof.

As used herein, the term “DUX-s” encompasses naturally occurring DUX4-s protein that is isolated from a human subject (i.e. SEQ ID NO:112, or a naturally occurring variant thereof, encoded by DUX4-s cDNA (Genbank No. HQ266762) (SEQ ID NO:111). The term “variant of DUX4-s” refers to a polypeptide comprising at least 90%, or at least 95%, or at least 99% identity to DUX4-s polypeptide, set forth as SEQ ID NO:112, including naturally occurring variants thereof.

As used herein, the term “FSHD gene marker” refers to an entire gene, or portion thereof, such as an EST derived from that gene, the expression or level of which (including mRNA or protein) is induced in the presence of DUX4-fl.

As used herein, the term “FSHD gene marker-derived polynucleotides” refers to the RNA transcribed from a marker gene, any cDNA or cRNA produced therefrom, and any nucleic acid derived therefrom, such as synthetic nucleic acid having a sequence derived from the gene corresponding to the marker gene.

As used herein, the term “biological sample” refers to any type of material of biological origin isolated from a subject, including, for example, DNA, RNA, protein, such as, for example, blood, plasma, serum, fecal matter, urine, semen, bone marrow, bile, spinal fluid, tears, saliva, muscle biopsy, organ tissue or other material of biological origin known by those of ordinary skill in the art.

As used herein, the term “antibody” encompasses antibodies and antibody fragments thereof, derived from any antibody-producing mammal (e.g., mouse, rat, rabbit, and primate including human), that specifically bind to FSHD biomarker polypeptides or portions thereof. Exemplary antibodies include polyclonal, monoclonal and recombinant antibodies; multispecific antibodies (e.g., bispecific antibodies); humanized antibodies; murine antibodies; chimeric, mouse-human, mouse-primate, primate-human monoclonal antibodies; and anti-idiotype antibodies, and may be any intact molecule or fragment thereof. As used herein, “a mammalian subject” includes all mammals, including without limitation humans, non-human primates, dogs, cats, horses, sheep, goats, cows, rabbits, pigs and rodents.

As used herein, the term “operatively linked” refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner. For example, a promoter sequence is operatively linked to a coding sequence if the promoter sequence promotes transcription of the coding sequence.

As used herein, the term “vector” is a nucleic acid molecule, preferably self-replicating, which transfers and/or replicates an inserted nucleic acid molecule into and/or between host cells.

As used herein, the term “nucleic acid sequences allowing for autonomous replication” refers to a polynucleotide comprising an origin of replication (generally referred to as an on sequence) which allows for replication of the polynucleotide in the appropriate host cell.

As used herein, the term “nucleic acid sequences allowing for selection” refers to polynucleotides encoding any protein that provides a phenotypic marker, for example, a protein that is necessary for cell growth, or resistance to a toxin, or a protein providing a surface antigen for which specific antibodies/ligands are available.

As used herein, the term “therapeutically effective amount” is an amount of an agent of the invention that alleviates, totally or partially, the pathophysiological effects of at least one of FSHD, myotonic dystrophy or Huntington's disease; or of an autoimmune disease such as Systemic Lupus Erythermatosis, Aicardi-Goutieres Syndrome or Multiple Sclerosis. The amount will depend on, for example, the subject size, gender, magnitude of the associated condition or injury, and the like. For a given subject in need thereof a therapeutically effective amount can be determined by those of ordinary skill in the art by methods known to those of ordinary skill in the art.

As used herein, the term “treat” and all its forms and tenses refer to both therapeutic treatment and prophylactic or preventative treatment.

I. FACIOSCAPULOHUMERAL DYSTROPHY (FSHD)

It has been known for about 20 years that FSHD is caused by the shortening of a macrosatellite repeat array on chromosome 4, but the molecular mechanism leading to muscle pathology has been elusive and controversial. It was recently determined that the DUX4 retrogene contained in these repeats is the likely cause of FSHD, based on genetic studies that identified polymorphisms that create a DUX4 polyadenylation site as necessary for a D4Z4 contraction to cause FSHD (Lemmers et al., 2010). It has also been shown that a subset of individuals with clinical features of FSHD do not have contracted D4Z4 repeats on chromosome 4 but do have decreased repressive heterochromatin at the D4Z4 repeats (de Greef et al., 2009) (FSHD2), indicating that loss of repressive chromatin at D4Z4 is the primary cause of FSHD. High sensitivity RT-PCR assays detect DUX4 mRNA specifically in FSHD muscle (Dixit et al., 2007; Snider et al., 2010). It has also been shown that DUX4 is normally expressed in germ cells and epigenetically repressed in healthy somatic tissues, but the occasional escape from epigenetic repression of FSHD muscle cells results in bursts of DUX4 in a small fraction of nuclei (Snider et al., 2010). Still, a major problem with the hypothesis that DUX4 expression causes FSHD has been the extremely low abundance of the mRNA and inability to reliably detect the protein in FSHD biopsy samples.

Our prior work demonstrated that the low abundance of DUX4 in FSHD muscle cells represents a relatively high expression in a small subset of nuclei (Snider et al., 2010, supra). However, it remained unclear whether the low expression of DUX4 in FSHD muscle has a biological consequence that might drive the pathophysiology of FSHD.

II. DUX4

DUX4 belongs to the double-homeobox transcription factor family, and the biological role of this large class of DNA-binding proteins is largely unknown. The coding sequence of the DUX4 retrogene has been conserved in primates (Clapp et al., 2007), but whether this retrogene has a normal physiological function is unknown. Previously the inventors found that DUX4 is normally expressed at high levels in germ cells of human testes and is epigenetically repressed in somatic tissues (Snider et al., 2010), whereas the epigenetic repression of the DUX4 locus in somatic tissues is less efficient in both FSHD1 and FSHD2, resulting in DUX4 expression in FSHD muscle cell nuclei. The germline-specific expression pattern of DUX4 is similar to that of other double homeodomain proteins (Booth and Holland, 2007; Wu et al., 2010). The function of this distinct family of DNA-binding proteins is unknown, but their shared tissue expression pattern may indicate a possible role for double homeodomain transcription factors in reproductive biology.

As described herein in Examples 1-3, the present inventors have now discovered that DUX4 regulates the expression of genes involved in germline and early stem cell development. As described herein, the genes regulated by DUX4 are reliably detected in FSHD muscle but not in controls, providing direct support for the model that misexpression of DUX4 is a causal factor for FSHD. As described in Example 1, through the use of expression arrays and chromatin immunoprecipitation combined with high throughput sequencing the inventors have identified DUX4 target genes that are bound and regulated by DUX4. As further described herein, DUX4 regulates germline and stem cell genes, which is consistent with its normal expression pattern and indicates a physiological role for DUX4 in germ cell and reproductive biology. As described in Example 2, the inventors identified the consensus binding site for DUX4, a double homeodomain motif, and further demonstrate that DUX4 binds to and activates transcription from endogenous retrotransposon LTRs of the MaLR family. As described in Example 3, the inventors have determined that the transcriptional targets of DUX4 are aberrantly expressed in biopsies of FSHD skeletal muscle but not in control muscle biopsies. Therefore, the low level of DUX4 expression in FSHD is sufficient to effect numerous downstream changes and activate genes of germ cell and early development in postmitotic skeletal muscle. These findings provide direct support for DUX4 as the causal factor for FSHD, and also provide valuable biomarkers to assess the presence or risk of FSHD, a disease that has been difficult to diagnose with genetic testing.

As described in Example 4, the inventors have determined that DUX4-fl activates expression of multiple cancer testis antigens and gene families in FSHD muscle and DUX4-fl expression correlates with expression of cancer testis antigens (CTAs) in a cancer cell and CTA family members are induced by DUX4-fl in dendritic cells.

As described in Example 5, the inventors have discovered that agents that increase chromatin mediated repression, such as agents that inhibit LSD1 activity, are useful to suppress DUX4 and are candidate therapeutic agents for FSHD. Such agents are believed to also have application to other diseases, such as myotonic dystrophy or Huntington's disease, where increasing chromatin mediated suppression of the mutant allele would have to herapeutic benefit. As further described in Example 5, the inventors have also discovered that an agent that modifies translation dependent nonsense mediated decay stabilizes DUX4 mRNA levels. Therefore, approaches that block translation dependent nonsense mediated decay can be used to increase DUX4 mRNA and agents that enhance nonsense mediated decay can be used to enhance the degradation of DUX4 mRNA, which provides a candidate therapy for FSHD.

As described in Example 6, DUX4 binds and activates LTR elements from a class of MaLR endogenous primate retrotransposons and suppresses the innate immune response to viral infection, at least in part through the activation of DEFB103, a human defensin that can inhibit muscle differentiation. These findings suggest specific mechanisms of FSHD pathology and identify biomarkers useful for disease diagnosis and progression.

As described in Example 7, siRNA knockdown of DUX4 confirmed that the activation of germline genes in FSHD muscle cells is due to the leaky expression of DUX4 in FSHD muscle cells. Therefore, agents that inhibit the activity of DUX4, either by eliminating its expression in the muscle cells, as done in vitro with an siRNA, or by introducing a dominant negative agent, such as the DUX4-s splice form are expected to be useful as therapeutic agents for treating and/or preventing FSHD, or symptoms related to FSHD.

As described in Example 8, DUX4 can prevent the innate immune response to viral infection in skeletal muscle cells, at least in part, through the transcriptional induction of DEFB103. As further described in Example 8, the inventors have discovered that DEFB103 suppresses the induction of skeletal muscle differentiation genes, beta-defensin 3 (DEFB103) inhibits muscle cell fusion and expression of myosin heavy chain in primary muscle.

III. METHODS OF INHIBITING THE INNATE IMMUNE RESPONSE IN A MAMMALIAN SUBJECT

In one aspect, the invention provides a method of inhibiting the innate immune response in a mammalian subject in need thereof, comprising administering to the mammalian subject an agent capable of inducing, or increasing the level of DUX4-fl expression in a population of cells in the mammalian subject.

In some embodiments of this aspect of the invention, the method comprises administering a therapeutic agent that is capable of inducing or increasing the level of endogenous DUX4-fl. In some embodiments, the therapeutic agent is a demethylating agent, such as 5-azacytidine (decatibine).

In some embodiments of this aspect of the invention, the method comprises administering a therapeutic agent that blocks translation dependent nonsense mediated decay, such as cycloheximide, or an inhibitor of UPF, such as the inhibitor of UPF described in Sun et al., 1998), hereby incorporated herein by reference or an inhibitory nucleic acid that specifically binds a UPF gene, such as UPF1 siRNA, or an agent that inhibits the kinase dependent activation of UPF1.

In some embodiments of this aspect of the invention, the method comprises administering DUX4-fl polypeptide or a nucleic acid encoding DUX4-fl polypeptide in a composition formulated for in vivo delivery to a mammalian subject.

In some embodiments, the agent capable of increasing or inducing DUX4-fl expression is administered to the mammalian subject in an amount sufficient to inhibit or reduce the expression of at least one or more of the three primary sensors of viral RNA LGP2 (DHX58), IFIH1 (MDA5), and/or DDX58 (RIG-1)). In some embodiments, the agent is administered to the mammalian subject in an amount sufficient to inhibit the innate immune response to a viral infection in the mammalian subject.

In one embodiment, the invention provides a method of inhibiting the innate immune response in a mammalian subject by administering to the subject an agent capable of inducing, or increasing the level of DEFB103A (SEQ ID NO:49), and/or DEFB103B (SEQ ID NO:107) expression in a population of cells in the mammalian subject. In some embodiments, the method comprises administering the DEFB103A/B polypeptide (SEQ ID NO:178), or a nucleic acid molecule encoding the polypeptide (SEQ ID NO:49 or SEQ ID NO:107) to the mammalian subject.

In certain embodiments, the level of DEFB103A/B is increased by about, at least about, or at most about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 400, 500, 600, 700, 800, 900, 1000% or more (or any range derivable therein) relative to the level in the absence of the agent.

The methods in accordance with this aspect of the invention can be used to suppress the immune response in order to induce immune tolerance, and may be used to treat a subject suffering from an autoimmune disease (e.g., Systemic Lupus Erythermatosis, Aicardi-Goutieres syndrome, or Multiple Sclerosis, or to prepare a subject for transplant, or treat a subject that is undergoing, or has undergone, an organ or tissue transplant.

In another aspect, the invention provides a method of suppressing or inhibiting the innate immune response in a mammalian subject in need thereof, comprising administering to the mammalian subject an agent capable of inducing, or increasing the level of DEFB103A and/or DEFB103B expression or activity in a population of cells in the mammalian subject. In some embodiments, the agent is capable of increasing endogenous DEFB103 mRNA expression in the cells. In some embodiments, the agent comprises a nucleic acid molecule (e.g., SEQ ID NO:49 and/or SEQ ID NO:107) encoding DEFB103 (SEQ ID NO:178). In some embodiments, the agent comprises the DEFB103 polypeptide (SEQ ID NO:178).

The method in accordance with this aspect of the invention can be used to treat a subject in need thereof selected from the group consisting of (i) a subject suffering from an autoimmune disease and (ii) a subject that is undergoing, or has undergone an organ or tissue transplant. In some embodiments, the autoimmune disease is selected from the group consisting of Systemic Lupus Erythermatosis, Aicardi-Goutieres syndrome and Multiple Sclerosis.

IV. METHODS OF INCREASING OR MAINTAINING THE INNATE IMMUNE RESPONSE IN A MAMMALIAN SUBJECT

In another aspect, the invention provides a method of increasing or maintaining the innate immune response in a mammalian subject in need thereof. The method in accordance with this aspect of the invention comprises administering to the mammalian subject an agent capable of inhibiting, or suppressing the level of DUX4-fl expression, or an agent capable of inhibiting DUX4-fl mediated transcription activation in a population of cells in the mammalian subject.

In some embodiments of this aspect of the invention, the method comprises administering a therapeutic agent that is capable of inhibiting or suppressing the level of endogenous DUX4-fl. In some embodiments, the agent is capable of increasing chromatin mediated repression, such as an agent that inhibits histone demethylase LSD1 activity (e.g., paragline). In some embodiments, the agent enhances nonsense mediated decay and thereby enhances the degradation of DUX4 mRNA.

In some embodiments, the agent is capable of inhibiting DUX4-fl mediated transcriptional activation is an agent that interferes with DUX4-fl binding to one or more DUX4-fl consensus binding site(s) “TAAYBBAATCA” (SEQ ID NO: 166) that is present upstream of one or more DUX4-fl inducible genes. An exemplary agent for use in accordance with this embodiment is a DUX4-s polypeptide, or a nucleic acid encoding DUX4-s polypeptide. In some embodiments, the invention provides a pharmaceutical composition comprising a DUX4-s polypeptide or a nucleic acid encoding a DUX4-s polypeptide and a pharmaceutically acceptable carrier.

The methods in accordance with this aspect of the invention can be used to enhance the immune response, and can be used to treat a subject suffering from, or at risk for developing FSHD, or a subject suffering from, or at risk for developing myotonic dystrophy or Huntington's disease, or a subject suffering from cancer, or a subject that is infected with a pathogen, such as a viral infection (e.g., HIV).

In another aspect, the invention provides methods for increasing or maintaining the innate immune response in a mammalian subject in need thereof, comprising administering to the mammalian subject an agent capable of inhibiting, or suppressing the level of DEFB103A and/or DEFB103B expression in a population of cells in the mammalian subject.

In some embodiments, the agent capable of inhibiting DEFB103 expression is an agent that interferes with DUX4-fl binding to one or more DUX4-fl consensus binding site(s) “TAAYBBAATCA” (SEQ ID NO: 166) that is present upstream of DEFB103 (which is an DUX4-fl inducible gene). An exemplary agent for use in accordance with this embodiment is a DUX4-s polypeptide, or a nucleic acid encoding DUX4-s polypeptide. In some embodiments, the invention provides a pharmaceutical composition comprising a DUX4-s polypeptide or a nucleic acid encoding a DUX4-s polypeptide and a pharmaceutically acceptable carrier.

In another embodiment, the agent capable of inhibiting DEFB103 expression is a nucleic acid molecule (e.g., antisense, siRNA,) that specifically hybridizes to a nucleic acid encoding DEFB103, such as SEQ ID NO; 49 and/or SEQ ID NO:107.

In another embodiment, the agent capable of inhibiting DEFB103 activity specifically binds to DEFB103A polypeptide (SEQ ID NO:178), such as an antibody, or fragment thereof that is capable of inhibiting or blocking DEFB103 activity. In another embodiment, the agent capable of inhibiting DEFB103 activity is a small molecule inhibitor.

In some embodiments, the agent for use in this aspect of the invention is an agent that is capable of reducing the level of endogenous DUX4-fl. In some embodiments, the agent enhances translation dependent nonsense mediated decay.

The methods in accordance with this aspect of the invention can be used to maintain and/or enhance the innate immune response or treat or prevent a disease in need of modulation of DUX4 or its target gene such as DEFB103A or DEFB103B. In certain aspects, the methods can be used to restore the expression or activity of DUX4 or its target gene to a normal level. In certain aspects, the modulation may be inhition of the expression or activity of DUX4 or its target gene if DUX4 or its target gene is present at or is determined to have a higher expression or activity as compared to a normal control; in other aspects, the modulation may upregulation of the expression or activity of DUX4 or its target gene if the expression or activity in the subject is lower than a normal control.

For example, the methods can be used to treat a subject selected from the group consisting of (i) a subject suffering from, or at risk for developing FSHD, (ii) a subject suffering from or at risk for developing myotonic dystrophy, (iii) a subject suffering from or at risk for developing Huntington's disease, (iv) a subject suffering from cancer, (v) a subject suffering from an autoimmune disease, and (vi) a subject infected with a pathogen, such as a virus, such as HIV.

V. METHODS OF MODULATING MYOGENESIS

In another aspect, the invention provides methods and compositions for modulating myogenesis in muscle cells.

In one embodiment, the invention provides a method of inhibiting myogenesis in muscle cells comprising contacting the cells with an agent capable of inducing or increasing the level of DEFB103. In some embodiments, the agent is capable of increasing endogenous DEFB103 mRNA expression in the cells. In some embodiments, the agent comprises a nucleic acid molecule encoding DEFB103. In some embodiments, the agent comprises DEFB103 polypeptide.

In another embodiment, the invention provides a method of promoting myogenesis in muscle cells comprising contacting the cells with an agent capable of inhibiting DEFB103 expression and/or DEFB103 activity. In some embodiments, the agent specifically binds to DEFB103A polypeptide or a nucleic acid encoding DEFB103A polypeptide. In some embodiments, the agent is capable of inhibiting DUX4-fl mediated transcriptional activation.

In another aspect, the invention provides a method of promoting or maintaining muscle differentiation in a mammalian subject in need thereof, comprising administering to the mammalian subject an agent capable of inhibiting, or suppressing the level of DEFB103 expression and/or inhibiting DEFB103 activity in a population of muscle cells in the mammalian subject. In some embodiments, the agent specifically binds to DEFB103A polypeptide or a nucleic acid encoding DEFB103A polypeptide. In some embodiments, the agent is capable of inhibiting DUX4-fl mediated transcriptional activation. In some embodiments, the subject in need thereof is selected from the group consisting of (i) a subject suffering from, or at risk for developing FSHD, (ii) a subject suffering from or at risk for developing myotonic dystrophy, (iii) a subject suffering from or at risk for developing Huntington's disease, (iv) a subject suffering from or at risk for developing muscular dystrophy, (v) a subject suffering from or at risk for developing sarcopenia.

VI. METHODS OF INDUCING TESTIS-EXPRESSED GENES IN NON-TESTIS CELL TYPES

In another aspect, the invention provides a method of inducing one or more testis expressed genes (e.g., cancer testis antigens) in a non-testis cell type comprising contacting the non-testis cell type with an agent capable of inducing, or increasing the level of DUX4-fl expression in a population of cells.

In some embodiments, the agent for use in this aspect of the invention is an agent that is capable of inducing or increasing the level of endogenous DUX4-fl. In some embodiments, the agent is a demethylating agent, such as 5-azacytidine (decatibine). In some embodiments, the agent blocks translation dependent nonsense mediated decay, such as cycloheximide.

In some embodiments, the agent is a DUX4-fl polypeptide or a nucleic acid encoding DUX4-fl polypeptide. In some embodiments, the invention provides a pharmaceutical composition comprising a DUX4-fl polypeptide or a nucleic acid encoding a DUX4-fl polypeptide and a pharmaceutically acceptable carrier.

The methods of this aspect of the invention may be carried out by contacting any type of non-testis cell type, including for example, skeletal muscle, cancer cells, and dendritic cells. The methods can be used in vitro or in vivo to enhance the immune response to the induced proteins for the purpose of expanding or activating T-cell populations, such as for anti-cancer therapies. This can be applied to immune therapy to stimulate T-cells to a cancer, or as a vaccine therapy to induce immunity to these antigens.

VII. PHARMACEUTICAL PREPARATIONS, CARRIERS AND DELIVERY VEHICLES

In general, the agents for use in the methods of the present invention, are suitably contained in a pharmaceutically acceptable carrier. The carrier is non-toxic, biocompatible and is selected so as not to detrimentally affect the biological activity of the agent. The agents of the invention may be formulated into preparations for local delivery (i.e. to a specific location of the body, such as skeletal muscle or other tissue) or systemic delivery, in solid, semi-solid, gel, liquid or gaseous forms such as tablets, capsules, powders, granules, ointments, solutions, depositories, inhalants and injections allowing for oral, parenteral or surgical administration. The invention also contemplates local administration of the compositions by coating medical devices and the like.

Suitable carriers for parenteral delivery via injectable, infusion or irrigation and topical delivery include distilled water, physiological phosphate-buffered saline, normal or lactated Ringer's solutions, dextrose solution, Hank's solution, or propanediol. In addition, sterile, fixed oils may be employed as a solvent or suspending medium. For this purpose any biocompatible oil may be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid find use in the preparation of injectables. The carrier and agent may be compounded as a liquid, suspension, polymerizable or non-polymerizable gel, paste or salve.

The carrier may also comprise a delivery vehicle to sustain (i.e., extend, delay or regulate) the delivery of the agent(s) or to enhance the delivery, uptake, stability or pharmacokinetics of the therapeutic agent(s). Such a delivery vehicle may include, by way of non-limiting example, microparticles, microspheres, nanospheres or nanoparticles composed of proteins, liposomes, carbohydrates, synthetic organic compounds, inorganic compounds, polymeric or copolymeric hydrogels and polymeric micelles.

The actual dosage amount of a composition of the present invention administered to a patient or subject can be determined by physical and physiological factors such as body weight, severity of condition, the type of disease being treated, previous or concurrent therapeutic interventions, idiopathy of the patient and on the route of administration. The practitioner responsible for administration will, in any event, determine the concentration of active ingredient(s) in a composition and appropriate dose(s) for the individual subject.

In certain embodiments, pharmaceutical compositions may comprise, for example, at least about 0.1% of an active compound, such as an isolated DUX4-fl polypeptide or DEFB103 polypeptide or their expression constructs, inhibitory antibodies or inhibitory nucleic acids. In other embodiments, the an active compound may comprise between about 2% to about 75% of the weight of the unit, or between about 25% to about 60%, for example, and any range derivable therein. In other non-limiting examples, a dose may also comprise from about 1 microgram/kg/body weight, about 5 microgram/kg/body weight, about 10 microgram/kg/body weight, about 50 microgram/kg/body weight, about 100 microgram/kg/body weight, about 200 microgram/kg/body weight, about 350 microgram/kg/body weight, about 500 microgram/kg/body weight, about 1 milligram/kg/body weight, about 5 milligram/kg/body weight, about 10 milligram/kg/body weight, about 50 milligram/kg/body weight, about 100 milligram/kg/body weight, about 200 milligram/kg/body weight, about 350 milligram/kg/body weight, about 500 milligram/kg/body weight, to about 1000 mg/kg/body weight or more per administration, and any range derivable therein. In non-limiting examples of a derivable range from the numbers listed herein, a range of about 5 μg/kg/body weight to about 100 mg/kg/body weight, about 5 microgram/kg/body weight to about 500 milligram/kg/body weight, etc., can be administered. A gene expression inhibitor may be administered in a dose of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100 or more μg of nucleic acid per dose. Each dose may be in a volume of 1, 10, 50, 100, 200, 500, 1000 or more μl or ml.

Solutions of therapeutic compositions can be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions also can be prepared in glycerol, liquid polyethylene glycols, mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms.

The therapeutic compositions of the present invention are advantageously administered in the form of injectable compositions either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid prior to injection may also be prepared. These preparations also may be emulsified. A typical composition for such purpose comprises a pharmaceutically acceptable carrier. For instance, the composition may contain 10 mg, 25 mg, 50 mg or up to about 100 mg of human serum albumin per milliliter of phosphate buffered saline. Other pharmaceutically acceptable carriers include aqueous solutions, non-toxic excipients, including salts, preservatives, buffers and the like.

Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oil and injectable organic esters such as ethyloleate. Aqueous carriers include water, alcoholic/aqueous solutions, saline solutions, parenteral vehicles such as sodium chloride, Ringer's dextrose, etc. Intravenous vehicles include fluid and nutrient replenishers. Preservatives include antimicrobial agents, anti-oxidants, chelating agents and inert gases. The pH and exact concentration of the various components the pharmaceutical composition are adjusted according to well known parameters.

Additional formulations are suitable for oral administration. Oral formulations include such typical excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate and the like. The compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders.

The therapeutic compositions of the present invention may include classic pharmaceutical preparations. Administration of therapeutic compositions according to the present invention will be via any common route so long as the target tissue is available via that route. This includes oral, nasal, buccal, rectal, vaginal or topical. Topical administration may be particularly advantageous for the treatment of skin cancers, to prevent chemotherapy-induced alopecia or other dermal hyperproliferative disorder. Alternatively, administration may be by orthotopic, intradermal, subcutaneous, intramuscular, intraperitoneal or intravenous injection. Such compositions would normally be administered as pharmaceutically acceptable compositions that include physiologically acceptable carriers, buffers or other excipients. For treatment of conditions of the lungs, aerosol delivery can be used. Volume of the aerosol is between about 0.01 ml and 0.5 ml.

An effective amount of the therapeutic composition is determined based on the intended goal. The term “unit dose” or “dosage” refers to physically discrete units suitable for use in a subject, each unit containing a predetermined-quantity of the therapeutic composition calculated to produce the desired responses discussed above in association with its administration, i.e., the appropriate route and treatment regimen. The quantity to be administered, both according to number of treatments and unit dose, depends on the protection or effect desired.

Precise amounts of the therapeutic composition also depend on the judgment of the practitioner and are peculiar to each individual. Factors affecting the dose include the physical and clinical state of the patient, the route of administration, the intended goal of treatment (e.g., alleviation of symptoms versus cure) and the potency, stability and toxicity of the particular therapeutic substance.

VIII. BIOMARKERS USEFUL FOR ASSESSING THE PRESENCE OR RISK OF DEVELOPING FSHD IN A MAMMALIAN SUBJECT

In one aspect, the invention provides a plurality of biomarkers useful for assessing the presence or risk of developing FSHD in a mammalian subject, wherein the FSHD biomarkers comprise a gene product of a DUX-4-fl induced gene, as set forth in TABLE 1 or TABLE 2. As described in Example 1, the inventors have determined that DUX4-fl (SEQ ID NO:110), encoded by DUX4-fl splice variant 1 cDNA (introns 1 and 2 are spliced) (Genbank No. HQ266760): (SEQ ID NO:108), or DUX4-fl splice variant 2 cDNA (intron 2 is spliced) (Genbank No. HQ266761): (SEQ ID NO:109), activates the expression of germline genes set forth in TABLE 1 and TABLE 2, referred to as “FSHD biomarkers.” The FSHD markers in TABLE 2 are a subset of the markers in TABLE 1. The gene products expressed from the gene markers listed in TABLES 1 and 2, or the polypeptides encoded by the gene markers, may be detected in accordance with the methods described herein for assessing the presence or risk of developing FSHD in a mammalian subject.

In some embodiments, the invention provides an isolated polynucleotide probe for detecting an FSHD biomarker, or a polynucleotide primer for amplifying at least a portion of an FSHD biomarker, wherein the nucleic acid probe or primer has a length of from at least 10 nucleotides to 200 nucleotides or longer, and specifically hybridizes to the nucleic acid sequence of at least one FSHD biomarker set forth in TABLE 1 or TABLE 2.

In some embodiments, the invention provides an isolated population of polynucleotide probes comprising a plurality of polynucleotides each complementary and hybridizable to a sequence of at least two or more (i.e. at least 3, 4, 5, 10, 15, 20, or more) different FSHD biomarkers selected from any one of TABLE 1 or TABLE 2. In some embodiments, the isolated population of polynucleotide probes are attached to a diagnostic tool for diagnosing or predicting the risk of developing FSHD in a human subject. In some embodiments, the polynucleotide probes are immobilized on a solid support, such as, for example a microarray. In one embodiment, the isolated population of polynucleotide probes comprise PCR primers for amplifying a portion of one or more FSHD biomarkers selected from TABLES 1 or 2. PCR primers are preferably chosen based on the sequence of the marker that will result in amplification of specific fragments of the marker gene. Computer programs that are well known in the art are useful in the design of primes with the required specificity and optimal amplification properties, such as Oligo version 5.0 (National Biosciences). PCR methods are well known in the art, and are described, for example, in Innis et al. (1990).

In another aspect, the invention provides one or more isolated antibodies that specifically bind to one or more FSHD polypeptide biomarker(s) encoded by the nucleic acid sequences set forth in TABLE 1 or TABLE 2. In some embodiments, the isolated antibodies further comprise a detectable label for use in a diagnostic assay. In some embodiments, one or more antibodies are bound to the surface of diagnostic tool (e.g., an immunoassay plate, a bead or a resin) for diagnosing or predicting the risk of developing FSHD in a human subject. The antibodies capable of binding to the polypeptides encoded by the one or more FSHD biomarkers can be polyclonal or monoclonal.

In certain embodiments, a diagnosis or risk assessment of FSHD can be made by analyzing the presence or amount of one or more FSHD biomarker polypeptide(s), by a variety of methods, including methods described herein, and also generally methods comprising spectroscopy, colorimetry, electrophoresis, isoelectric focusing, immunoprecipitations, and immunofluorescence, and immunoassays (e.g., David et al., U.S. Pat. No. 4,376,110) such as, for example immunoblotting (see also Current Protocols in Molecular Biology, particularly chapter 10).

Both quantitative and qualitative increases of the FSHD biomarker polypeptides are encompassed by the present invention. For example, in a particular embodiment, an antibody capable of binding to the polypeptide, preferably an antibody with a detectable label or an antibody that can be detected by a secondary antibody, can be used.

Antibodies can be polyclonal or monoclonal, and may be generated according to well known methods in the art, for example, monoclonal antibodies can be prepared, for example, using hybridoma technology (Köhler and Milstein, 1975).

An antibody in certain aspects of the present invention can be an intact immunoglobulin derived from natural sources or from recombinant sources, and can be immunoreactive portions of an intact immunoglobulin (including, for example, an antibody fragment and a single chain antibody). An antibody is typically a tetramer of immunoglobulin molecules. An antibody of the present invention can be prepared by a variety of methods (Coligan et al., 1991). For example, cells expressing a polypeptide of the present invention are administered to an animal to induce the production of sera containing polyclonal antibodies.

In particular aspects, a preparation of the secreted protein is prepared and purified to render it substantially free of natural contaminants. Such a preparation is then introduced into an animal in order to produce polyclonal antisera of greater specific activity.

In particular embodiments, an antibody of the present invention is a monoclonal antibody (mAb), or protein binding fragment thereof. Such monoclonal antibody can be prepared, for example, using hybridoma technology (Köhler and Milstein, 1975; Köhler and Milstein, 1976; Köhler et al., 1976; Monoclonal Antibodies and T-Cell Hybridomas, Elsevier, N.Y., pp. 563-681, 1981). In general, such methods involve immunizing an animal (e.g., a mouse) with polypeptide or with a secreted polypeptide-expressing cell. The splenocytes of, for example, such mice following the methods described above are extracted and fused with a suitable myeloma cell-line. The hybridoma cells obtained through such a selection are then assayed to identify clones that secrete antibodies capable of binding the polypeptide. An intact antibody, or a fragment thereof (e.g., Fab or F (ab′) 2) can be used. The term “labeled” with regard to the probe or antibody, is intended to encompass direct labeling of the antibody by coupling (i.e., physically linking) a detectable substance to the antibody, as well as indirect labeling of the antibody by reactivity with another reagent that is directly labeled or indirectly labeled. Examples of direct and indirect labels include, for example, a fluorescent moiety, an enzyme, a chromophoric moiety, a radioactive atom, a biotin tag, or a colorimetric tag. Some examples of a fluorescent moiety include rhodamine, fluorescein, etc. Some examples of enzymes include, horseradish peroxidase, glucose oxidase, glucose-6-phosphate dehydrogenase, alkaline phosphatase, beta-galactosidase, urease, luciferase, etc. Some examples of radioactive atoms are ³²P, ¹²⁵I, ³H, etc.

In some methods, a patient is identified as having one or more biomarkers indicative of FSHD or of being at risk for FSHD. In further embodiments, there is a step of reporting the patient as having one or more biomarkers indicative of FSHD or of being at risk for FSHD. Alternatively, in other embodiments there is a step of reporting the presence or absence of a biomarker or reporting the level of the biomarker. Additional embodiments include reporting to the subject or patient or to a treating clinician the results of any analysis or determination. Such reporting can involve an electronic or physical document.

Methods may also involve comparing a level of a biomarker to a control or reference level that reflects either the level of a patient who has FSHD or is at risk of FSHD or to a patient who does not have FSHD or who is not at risk for FSHD.

In additional embodiments, a patient identified as having or being at risk for FSHD may be treated accordingly. Further embodiments may involve knowing that a patient or subject is at risk for FSHD based on an analysis or determination discussed herein and subsequently treating or counseling the patient accordingly. A clinician may discuss lifestyle options to minimize muscle damage, career counseling and/or genetic counseling. These things may occur after a subject or patient is identified as having or being at risk for FSHD.

In another aspect, the invention provides a kit comprising one or more detection reagents for detecting one or more FSHD biomarkers set forth in TABLE 1 or TABLE 2 for use in an assay to determine the presence or risk of FSHD in a biological sample obtained from a mammalian subject. Reagents that are suited for obtaining a sample from an individual may be included in a kit of the invention, such as a syringe, collection vial, needle, or other instruments necessary to take a biopsy or other relevant sample. The kits may comprise a suitably aliquoted composition and/or additional agent compositions of the present invention, whether labeled or unlabeled, as may be used to prepare a standard curve for a detection assay. The components of the kit may be packaged in combination or alone in the same or in separate containers, depending on, for example, cross-reactivity or stability, and can also be supplied in solid, liquid, lyophilized, or other applicable form. The container means of the kits will generally include, for example, at least one vial, test tube, flask, bottle, syringe or other container means, into which a component may be placed, and preferably, suitably aliquoted. Where there is more than one component in the kit, the kit can contain a second, third or other additional container into which the additional components may be contained. However, various combinations of components may be comprised in a vial. The kits of the present invention also will typically include a means for containing the composition, additional agent and any other reagent containers in close confinement for commercial sale. Such containers may include, for example, injection or blow molded plastic containers into which the desired vials are retained.

IX. METHODS OF DETERMINING THE PRESENCE OF FSHD, OR RISK OF DEVELOPING FSHD IN A MAMMALIAN SUBJECT

In one aspect, the invention provides a method of determining the presence of, or risk of developing, Facioscapulohumeral dystrophy (FSHD) in a mammalian subject. The method in accordance with this aspect comprises: (a) determining the presence or amount of at least one FSHD biomarker in a biological test sample obtained from a mammalian subject, wherein the at least one FSHD biomarker comprises a gene product of a DUX-4-fl induced gene; and (b) comparing the presence or amount of the biomarker determined in step (a) with a reference standard or control sample, wherein an increase in the presence or amount of the FSHD biomarker determined in the test sample in comparison to the reference standard or control sample is indicative of the presence of FSHD, or increased risk of developing FSHD, in the mammalian subject.

In some embodiments, the DUX4-fl induced gene is expressed from a promoter comprising at least one or more DUX-4 responsive elements comprising the consensus sequence “TAAYBBAATCA” (SEQ ID NO:166). In some embodiments, the at least one DUX4-fl induced gene product (mRNA or polypeptide) is expressed at an increased level of at least 2-fold or greater (i.e. at least 3-fold, at least 5-fold, at least 8-fold, at least 10-fold, at least 16 fold or greater) in FSHD skeletal muscle as compared to normal control skeletal muscle. In some embodiments, the method comprises determining the presence or amount of at least one or more FSHD biomarkers selected from TABLE 1 or TABLE 2 in a biological test sample by contacting the sample with a detection reagent (e.g., a PCR primer or antibody) that specifically detects a nucleic acid (e.g., mRNA) or polypeptide expressed from, or derived from, the FSHD biomarker.

In some embodiments, the method comprises determining the presence or amount of a nucleic acid or polypeptide expressed from, or derived from, at least one DUX4-fl induced gene selected from the group consisting of: TRIM43 (SEQ ID NO:62), TRIM48 (SEQ ID NO:23), KHDC1 (SEQ ID NO:21), MBD3L2 (SEQ ID NO:29), PRAMEF1 (SEQ ID NO:16), PRAMEF2 (SEQ ID NO:28), ZSCAN4 (SEQ ID NO:5), RFPL2 (SEQ ID NO:36), CCNA1 (SEQ ID NO:31), DEFB103A (SEQ ID NO:49), and DEFB103B (SEQ ID NO:107).

In some embodiments, the method comprises performing quantitative RT-PCR on the biological sample with reagents that specifically hybridize to the mRNA expressed from the DUX4-fl induced gene. In some embodiments, the method comprises contacting the biological test sample with an antibody that specifically binds to the at least one biomarker. In some embodiments, the method comprises analyzing the biological sample with mass spectrometry to detect the presence or amount of the at least one biomarker.

In some embodiments, the method comprises determining the presence or amount of two or more different FSHD biomarkers (i.e., at least 3, 4, 5, 10, 15, 20, or more) selected from any one of TABLE 1 or TABLE 2 in the biological test sample.

In some embodiments, the biological test sample is obtained from a mammalian living fetus, such as a living human fetus. In some embodiments, the biological test sample is obtained from a subject suspected of having FSHD. In some embodiments, the biological test sample is obtained from a subject with a family member diagnosed with FSHD. In some embodiments, the biological test sample is obtained from a subject known to have FSHD, for example, in an embodiment in which the method is used for monitoring disease activity or progression, or response to therapy in a clinical trial or during therapeutic intervention.

In some embodiments, the biological test sample is selected from the group consisting of a muscle biopsy, blood, plasma, serum, urine, saliva, tears,

In accordance with the practice of various embodiments of the invention, polynucleotide molecules are extracted from a biological sample taken from a mammalian subject. The sample may be collected in any clinically acceptable manner, but must be collected such that marker-derived polynucleotides (i.e., RNA) are preserved and/or marker-derived polypeptides are preserved. In some embodiments, mRNA or nucleic acids derived therefrom (i.e., cDNA or amplified DNA) are preferably labeled distinguishably from standard or control polynucleotide molecules, and both are simultaneously or independently hybridized to a nucleic acid array, such as a microarray comprising some or all of the markers or marker sets or subsets described above. Alternatively, mRNA or nucleic acids derived therefrom may be labeled with the same label as the standard or control polynucleotide molecules, wherein the intensity of hybridization of each at a particular probe is compared. Methods for preparing total and poly(A)+RNA are well known and are described generally in Sambrook et al. (1989) and Ausubel et al. (1994).

In accordance with the methods of the invention, the presence or amount of the at least one FSHD biomarker in the test biological sample is compared with a reference standard or control sample, wherein an increase in the presence or amount of the FSHD biomarker determined in the test sample in comparison to the reference standard or control sample is indicative of the presence of FSHD, or increased risk of developing FSHD, or predict disease onset in the mammalian subject. In some embodiments, an increase in the presence or amount of the FSHD biomarker provides a clinical diagnosis of FSHD. In some embodiments, an increase in the presence or amount of the FSHD biomarker is indicative of disease progression. In some embodiments, a decrease in the amount of the FSHD biomarker is indicative of improvement of pathology in response to a therapeutic agent.

In one embodiment, the reference standard is the level of the one or more FSHD biomarkers measured in one or more biological sample(s) obtained from healthy control subjects known not to have FSHD. One or more, including 2, 3, 4, 5, 10 or more healthy individuals can be used to generate a reference standard for use in the methods. When multiple individuals are used to generate a reference standard for a particular FSHD biomarker, the biomarker levels determined from the individuals can be averaged to create a single reference standard value.

In another embodiment, the reference standard is an established threshold level. In one embodiment, the methods comprises the use of a control sample which may be obtained from a healthy subject.

In some embodiments, a determination is made that the mammalian subject from which the test sample was obtained has FSHD, or has an increased risk of developing FSDH, when the FSDH biomarker is found to be expressed at an increased level of at least 2-fold or greater (i.e. at least 3-fold, at least 4-fold, at least 5-fold, at least 8-fold, at least 10-fold, at least 12-fold, at least 16-fold or greater) in the test biological sample (e.g., skeletal muscle) as compared to the control or reference standard (e.g., normal skeletal muscle).

In another aspect, the invention provides a nucleic acid molecule comprising an expression cassette comprising a promoter operationally linked to a reporter gene or selectable marker, wherein the promoter contains at least one DUX4-responsive element (i.e., one, two, three, four or more) comprising the consensus sequence “TAAYBBAATCA” (SEQ ID NO:166). The reporter gene may be any suitable reporter gene used in the art. Non-limiting Examples of such reporter genes include chloramphenicol acetyl transferase (CAT) or luciferase. Non-limiting examples of suitable promoters include viral promoters such as a CMV or SV40 promoter. In some embodiments, the expression cassette is contained on an expression vector. In some embodiments, the expression cassette is present in a mammalian cell.

In another aspect, the invention provides a method of detecting the presence of DUX4-fl protein in a cell sample comprising introducing a nucleic acid molecule comprising an expression cassette comprising a promoter operationally linked to a reporter gene or selectable marker, wherein the promoter contains at least one DUX4-responsive element comprising the consensus sequence “TAAYBBAATCA” (SEQ ID NO:166), and assaying the cell for expression of the reporter gene, or selecting for growth under conditions requiring expression of the selectable marker, wherein expression of the reporter gene or growth under conditions requiring expression of the selectable marker indicate the presence of DUX4-fl protein.

In another aspect, the invention provides a method of identifying an inhibitor of DUX4-fl induced expression. The methods according to this aspect comprise: (a) contacting a cell containing: (i) a nucleic acid molecule comprising an expression cassette comprising a promoter operationally linked to a reporter gene or selectable marker, wherein the promoter contains at least one DUX4-responsive element comprising the consensus sequence “TAAYBBAATCA” (SEQ ID NO:166), and (ii) DUX4-fl polypeptide, with a candidate inhibitory agent; and (b) determining whether the cell expresses the reporter gene or selectable marker in the presence and absence of the candidate inhibitory agent, wherein the absence of expression of the reporter gene or selectable marker in the presence of the inhibitory agent indicates that the agent is an inhibitor of DUX4-fl induced expression. Candidate inhibitor compounds which may be used in accordance with this aspect of the invention may be natural or synthetic chemical compounds used in drug screening programmes (i.e. small molecules), or may be polypeptides (i.e. inhibitory peptides or antibodies).

X. MODULATION OF GENE EXPRESSION OR ACTIVITY

Aspects of the invention include modulating expression or activity of genes, such as DUX4, or its target genes, particularly DEFB103A or DEFB103B, in cells, tissues, or organs of a subject. Depending on the particular treatment purposes, the modulation may include inhibiting gene expression or activity by introducing inhibitory peptides or inhibitory nucleic acids to the subject, or increasing gene expression or activity by introducing isolated polypeptides or exogenous expression constructs or by increasing the endogenous gene expression.

A. Inhibition of Gene Expression or Activity

1. Inhibitory Peptides

In certain aspects, methods and compositions may be provided to inhibit the activity of particular polypeptides or peptides in a cell, for example, by molecules that specifically binds DUX4-fl or peptides encoded by its target genes, or specifically binds DUX4-responsive elements on its target genes but has reduced or no activity for regulating target genes as compared to native DUX4-fl (such as a dominant negative mutant). Such molecules may be an antibody, an isolated polypeptide or peptide, a synthetic peptide or a small molecule. The antibody may be selected from the group consisting of a chimeric antibody, an affinity matured antibody, a polyclonal antibody, a monoclonal antibody or a humanized antibody, and a human antibody. In a particular example, the antibody is a monoclonal antibody or a humanized antibody. In another example, the antibody is a polyclonal antibody. For example, a dominant negative mutant for DUX4-fl may be a DUX4 truncated form that lacks the transcriptional activation domain (such as DUX4-s)

In one embodiment, the antibody is a chimeric antibody, for example, an antibody comprising antigen binding sequences from a non-human donor grafted to a heterologous non-human, human or humanized sequence (e.g., framework and/or constant domain sequences). In one embodiment, the non-human donor is a mouse. In one embodiment, an antigen binding sequence is synthetic, e.g., obtained by mutagenesis (e.g., phage display screening, etc.). In one embodiment, a chimeric antibody of the invention has murine V regions and human C region. In one embodiment, the murine light chain V region is fused to a human kappa light chain. In one embodiment, the murine heavy chain V region is fused to a human IgG1 C region.

Examples of antibody fragments suitable for the present invention include, without limitation: (i) the Fab fragment, consisting of VL, VH, CL and CH1 domains; (ii) the “Fd” fragment consisting of the VH and CH1 domains; (iii) the “Fv” fragment consisting of the VL and VH domains of a single antibody; (iv) the “dAb” fragment, which consists of a VH domain; (v) isolated CDR regions; (vi) F(ab′)2 fragments, a bivalent fragment comprising two linked Fab fragments; (vii) single chain Fv molecules (“scFv”), wherein a VH domain and a VL domain are linked by a peptide linker which allows the two domains to associate to form a binding domain; (viii) bi-specific single chain Fv dimers (see U.S. Pat. No. 5,091,513) and (ix) diabodies, multivalent or multispecific fragments constructed by gene fusion (US Patent App. Pub. 20050214860). Fv, scFv or diabody molecules may be stabilized by the incorporation of disulphide bridges linking the VH and VL domains. Minibodies comprising a scFv joined to a CH3 domain may also be made (Hu et al, 1996).

Methods have been developed to replace light and heavy chain constant domains of the monoclonal antibody with analogous domains of human origin, leaving the variable regions of the foreign antibody intact. Alternatively, “fully human” monoclonal antibodies are produced in mice transgenic for human immunoglobulin genes. Methods have also been developed to convert variable domains of monoclonal antibodies to more human form by recombinantly constructing antibody variable domains having both rodent and human amino acid sequences. In “humanized” monoclonal antibodies, only the hypervariable CDR is derived from mouse monoclonal antibodies, and the framework regions are derived from human amino acid sequences. It is thought that replacing amino acid sequences in the antibody that are characteristic of rodents with amino acid sequences found in the corresponding position of human antibodies will reduce the likelihood of adverse immune reaction during therapeutic use. A hybridoma or other cell producing an antibody may also be subject to genetic mutation or other changes, which may or may not alter the binding specificity of antibodies produced by the hybridoma.

It is possible to create engineered antibodies, using monoclonal and other antibodies and recombinant DNA technology to produce other antibodies or chimeric molecules which retain the antigen or epitope specificity of the original antibody, i.e., the molecule has a binding domain. Such techniques may involve introducing DNA encoding the immunoglobulin variable region or the CDRs of an antibody to the genetic material for the framework regions, constant regions, or constant regions plus framework regions, of a different antibody. See, for instance, U.S. Pat. Nos. 5,091,513, and 6,881,557, which are incorporated herein by this reference.

2. Inhibitory Nucleic Acids

In certain aspects of the present invention, inhibitors for DUX4-fl and its target genes (such as DEFB103A or DEFB103B) may be used for treating a subject. For example, an DUX4-specific inhibitory nucleic acid or an inhibitory nucleic acid for UPF1 a may be used.

Examples of an inhibitory nucleic acid include but are not limited to siRNA (small interfering RNA), short hairpin RNA (shRNA), double-stranded RNA, an antisense oligonucleotide, a ribozyme and a nucleic acid encoding thereof.

In another embodiment, the inhibitory nucleic acid such as an siRNA molecule of a DUX4-fl gene or a related gene (as a template) has a sequence that is at least 75, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identity, preferably 95%, 99%, or 100% identity, to at least 10, 20, 50, 100, or 200 contiguous nucleotides of the nucleic acid sequences of a template. Without undue experimentation and using the disclosure of this invention, it is understood that additional siRNAs that modulate a template gene's expression can be designed and used to practice the methods of the invention.

An inhibitory nucleic acid may inhibit the transcription of a gene or prevent the translation of a gene transcript in a cell. An inhibitory nucleic acid may be from 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 60, 70, 80, 100, 200, 300, 400, 500, 600, 700, 800, 900, to 1000 nucleotides long, and in certain embodiments from 18 to 100 nucleotides long.

Particularly, an inhibitory nucleic acid or analog may be capable of decreasing the expression of a target gene, such as DUX4 or its target gene such as DEFB103A/B or its upstream regulator UPF1, by at least 10%, 20%, 30%, or 40%, more particularly by at least 50%, 60%, or 70%, and most particularly by at least 75%, 80%, 90%, 95% or more or any ranges in between the foregoing.

Inhibitory nucleic acids are well known in the art. For example, siRNA and double-stranded RNA have been described in U.S. Pat. Nos. 6,506,559 and 6,573,099, as well as in U.S. Patent Publications 2003/0051263, 2003/0055020, 2004/0265839, 2002/0168707, 2003/0159161, and 2004/0064842, all of which are herein incorporated by reference in their entirety.

For example, the inhibitory nucleic acid may be siRNA. siRNA can be obtained from commercial sources, natural sources, or can be synthesized using any of a number of techniques well-known to those of ordinary skill in the art. For example, commercial sources of predesigned siRNA include Invitrogen's Stealth™ Select technology (Carlsbad, Calif.), Ambion® (Austin, Tex.), and Qiagen® (Valencia, Calif.). An inhibitory nucleic acid that can be applied in the compositions and methods of the present invention may be any nucleic acid sequence that has been found by any source to be a validated down-regulator of a corresponding gene.

Certain embodiments of the present invention pertain to methods of inhibiting expression of DUX4-fl and its target genes in a cell by introduction of inhibitory nucleic acids or analogs into the cell. Introduction of nucleic acids or analogs into cells can be achieved by methods known in the art, including for example, microinjection, electroporation, or transfection of a vector comprising a nucleic acid from which the siRNA can be transcribed. Alternatively, an inhibitory nucleic acid or analog can be directly introduced into a cell in a form that is capable of binding to target desired mRNA transcripts. To increase durability and membrane-permeability the inhibitory nucleic acid or analog may be combined or modified with liposomes, poly-L-lysine, lipids, cholesterol, lipofectine or derivatives thereof. In a particular aspect, the inhibitory nucleic acid analog may be an antisense morpholino molecule.

3. Other Inhibitory Agents

In some embodiments of this aspect of the invention, the method comprises administering a therapeutic agent that is capable of inhibiting or suppressing the level of endogenous DUX4-fl.

In some embodiments, the agent is capable of increasing chromatin mediated repression, such as an agent that inhibits histone demethylase LSD1 activity (e.g., pargyline). Pargyline (Eutonyl; N-Benzyl-N-methylprop-2-yn-1-amine) is an irreversible monoamine oxidase B (MAO-B) inhibitor.

In some embodiments, the agent enhances nonsense mediated decay and thereby enhances the degradation of DUX4 mRNA.

B. Enhancement of Gene Expression or Activity

1. Enhancement of Endogenous Expression

In some embodiments of this aspect of the invention, the method comprises administering a therapeutic agent that blocks or reduces translation-dependent nonsense mediated decay, such as cycloheximide (a protein synthesis inhibitor), or an inhibitor of UPF, such as the inhibitor of UPF described in Sun et al. (1998), hereby incorporated herein by reference, or an agent that inhibits the kinase dependent activation of UPF1.

2. Isolated Polypeptides

In certain aspects, the invention is directed to a pharmaceutical composition comprising DUX4-fl polypeptide or peptides encoded by DUX4-fl target genes, such as DEFB103A or DEFB103B, or a peptide or polypeptide derived there from. It is contemplated that the compositions and methods disclosed herein may be utilized to express all or part of sequences selected from the group consisting of SEQ ID NOs:1-107 (TALE 2) and derivatives thereof. The structure of the various polypeptides or peptides can be modeled or resolved by computer modeling, NMR, or x-ray crystallography. Such structures may be used to engineer derivatives of a particular native protein.

The following is a discussion based upon changing of the amino acids of a native polypeptide described herein to create an equivalent, or even an improved, second-generation molecule. For example, certain amino acids may be substituted for other amino acids in a protein structure without appreciable loss of interactive binding capacity with structures such as, for example, antigen-binding regions of antibodies or binding sites on substrate molecules. Since it is the interactive capacity and nature of a protein that defines that protein's biological functional activity, certain amino acid substitutions can be made in a protein sequence, and in its underlying DNA or RNA coding sequence, and nevertheless produce a protein with like properties. It is thus contemplated by the inventors that various changes may be made in the DNA or RNA sequences of genes or coding regions without appreciable loss of their biological utility or activity, as discussed herein.

Various types of expression vectors are known in the art that can be used for the production of protein or peptide products. For example, following transfection with a expression vector comprising a coding sequence selected from the group consisting of SEQ ID NOs:1-107 to a cell in culture, e.g., a primary mammalian cell, a recombinant protein product may be prepared in various ways. A host cell strain may be chosen that modulates the expression of the inserted sequences, or that modifies and processes the gene product in the manner desired. Such modifications (e.g., glycosylation) and processing (e.g., cleavage) of protein products may be important for the function of the protein. Different host cells have characteristic and specific mechanisms for the post-translational processing and modification of proteins. Appropriate cell lines or host systems can be chosen to insure the correct modification and processing of the foreign protein expressed. In order for the cells to be kept viable while in vitro and in contact with the expression construct, it is necessary to ensure that the cells maintain contact with the correct ratio of oxygen and carbon dioxide and nutrients but are protected from microbial contamination.

Certain aspects of the present invention concern the purification, and in particular embodiments, the substantial purification, of an encoded protein or peptide. The term “isolated or purified protein or peptide” as used herein, is intended to refer to a composition, isolatable from other components, wherein the protein or peptide is purified to any degree relative to its naturally obtainable state. A isolated or purified protein or peptide therefore also refers to a protein or peptide, free from the environment in which it may naturally occur.

3. Exogenous Expression Constructs

Aspects of the invention include introducing into a cell with an expression construct comprising at least a particular peptide, such as DUX4-fl polypeptide or peptides encoded by DUX4-fl target genes, such as DEFB103A or DEFB103B. In other aspects, expression construct may include one or more additional nucleic acid sequences, such as additional reporters, additional coding regions, or additional promoters.

In certain embodiments of the present invention, transfer of an expression construct into a cell is accomplished using a viral vector. Techniques using “viral vectors” are well-known in the art. A viral vector is meant to include those constructs containing viral sequences sufficient to (a) support packaging of the expression cassette and (b) to ultimately express a recombinant gene construct that has been cloned therein.

Several non-viral methods for the transfer of nucleic acids into cells also are contemplated by certain aspects of the present invention. These include calcium phosphate precipitation (Graham and Van Der Eb, 1973; Chen and Okayama, 1987; Rippe et al, 1990) DEAE-dextran (Gopal, 1985), electroporation (Tur-Kaspa et al, 1986; Potter et al, 1984), nucleofection (Trompeter et al, 2003), direct microinjection (Harland and Weintraub, 1985), DNA-loaded liposomes (Nicolau and Sene, 1982; Fraley et al, 1979) and lipofectamine-DNA complexes, polyamino acids, cell sonication (Fechheimer et al, 1987), gene bombardment using high velocity microprojectiles (Yang et al, 1990), polycations (Boussif et al, 1995) and receptor-mediated transfection (Wu and Wu, 1987; Wu and Wu, 1988). Some of these techniques may be successfully adapted for in vivo or ex vivo use. A person of ordinary skill in the art would be familiar with the techniques pertaining to use of nonviral vectors, and would understand that other types of nonviral vectors than those disclosed herein are contemplated by the present invention. In a further embodiment of the invention, the expression cassette may be entrapped in a liposome or lipid formulation. Liposomes are vesicular structures characterized by a phospholipid bilayer membrane and an inner aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. Also contemplated is a gene construct complexed with Lipofectamine (Gibco BRL). One of ordinary skill in the art would be familiar with techniques utilizing liposomes and lipid formulations.

XI. DISEASES

Diseases to be prevented, treated or diagnosed can be any disease that affects a subject that would be amenable to therapy or prevention through administration of a composition or a therapeutic agent as described herein. For example, the disease may be a disease amenable to the therapy for modulation of DUX4-fl expression or activity or its target genes such as DEFB103A/B. In particular examples, there may provided methods and compositions involving inhibition or suppression of DUX4-fl or its target gene DEFB103A/B for treating muscular dystrophy or myotonic dystrophy.

Examples include muscular diseases, cancer, infections, diabetes, cardiovascular disease, neurological disease, neurodegenerative disease, genetic disease, liver disease, infection, trauma, toxicity, or immunological disease.

A. Muscular Dystrophy

According to an embodiment of the invention, the methods described herein are useful in inhibiting the development of and/or treating muscular dystrophy or myotonic dystrophy. In a specific embodiment, treatment is by inhibiting or reducing the expression of DUX4-fl or DEFB103A/B.

Muscular dystrophy (MD) is a group of muscle diseases that weaken the musculoskeletal system and hamper locomotion. Muscular dystrophies are characterized by progressive skeletal muscle weakness, defects in muscle proteins, and the death of muscle cells and tissue.

It soon became evident that the disease had more than one form. In addition to Duchenne muscular dystrophy, the other major forms are Becker, limb-girdle, congenital, facioscapulohumeral, myotonic, oculopharyngeal, distal, and Emery-Dreifuss muscular dystrophy. These diseases predominately affect males, although females may be carriers of the disease gene. Most types of MD are multi-system disorders with manifestations in body systems including the heart, gastrointestinal system, nervous system, endocrine glands, eyes and brain.

Apart from the nine major types of muscular dystrophy listed above, several MD-like conditions have also been identified. Normal intellectual, behavioral, bowel and sexual function is noticed in individuals with other forms of MD and MD-like conditions. MD-affected individuals with susceptible intellectual impairment are diagnosed through molecular characteristics but not through problems associated with disability. However, a third of patients who are severely affected with MD may have cognitive impairment, behavioral, vision and speech problems.

Myotonic dystrophy (dystrophia myotonica, myotonia atrophica) is a chronic, slowly progressing, highly variable, inherited multisystemic disease. It is characterized by wasting of the muscles (muscular dystrophy), cataracts, heart conduction defects, endocrine changes, and myotonia. Two types of myotonic dystrophy exist.

Myotonic dystrophy type 1 (DM1), also called Steinert disease, has a severe congenital form and a milder childhood-onset form. Myotonic dystrophy type 2 (DM2), also called proximal myotonic myopathy (PROMM) or adult-onset form, is rarer than DM1 and generally manifests with milder signs and symptoms. Myotonic dystrophy can occur in patients of any age. Both forms of the disease display an autosomal dominant pattern of inheritance.

B. Cancer

The present invention may be used to treat a disease, such as cancer. For example, a pharmaceutical preparation may be delivered to treat a cancer. The cancer may be a solid tumor, metastatic cancer, or non-metastatic cancer. In certain embodiments, the cancer may originate in the bladder, blood, bone, bone marrow, brain, breast, colon, esophagus, gastrointestine, gum, head, kidney, liver, lung, nasopharynx, neck, ovary, prostate, skin, stomach, testis, tongue, or uterus. In certain embodiments, the cancer is human ovarian cancer. In addition, the cancer may specifically be of the following histological type, though it is not limited to these: neoplasm, malignant; carcinoma; carcinoma, undifferentiated; giant and spindle cell carcinoma; small cell carcinoma; papillary carcinoma; squamous cell carcinoma; lymphoepithelial carcinoma; basal cell carcinoma; pilomatrix carcinoma; transitional cell carcinoma; papillary transitional cell carcinoma; adenocarcinoma; gastrinoma, malignant; cholangiocarcinoma; hepatocellular carcinoma; combined hepatocellular carcinoma and cholangiocarcinoma; trabecular adenocarcinoma; adenoid cystic carcinoma; adenocarcinoma in adenomatous polyp; adenocarcinoma, familial polyposis coli; solid carcinoma; carcinoid tumor, malignant; branchiolo-alveolar adenocarcinoma; papillary adenocarcinoma; chromophobe carcinoma; acidophil carcinoma; oxyphilic adenocarcinoma; basophil carcinoma; clear cell adenocarcinoma; granular cell carcinoma; follicular adenocarcinoma; papillary and follicular adenocarcinoma; nonencapsulating sclerosing carcinoma; adrenal cortical carcinoma; endometroid carcinoma; skin appendage carcinoma; apocrine adenocarcinoma; sebaceous adenocarcinoma; ceruminous adenocarcinoma; mucoepidermoid carcinoma; cystadenocarcinoma; papillary cystadenocarcinoma; papillary serous cystadenocarcinoma; mucinous cystadenocarcinoma; mucinous adenocarcinoma; signet ring cell carcinoma; infiltrating duct carcinoma; medullary carcinoma; lobular carcinoma; inflammatory carcinoma; paget's disease, mammary; acinar cell carcinoma; adenosquamous carcinoma; adenocarcinoma w/squamous metaplasia; thymoma, malignant; ovarian stromal tumor, malignant; thecoma, malignant; granulosa cell tumor, malignant; androblastoma, malignant; sertoli cell carcinoma; leydig cell tumor, malignant; lipid cell tumor, malignant; paraganglioma, malignant; extra-mammary paraganglioma, malignant; pheochromocytoma; glomangiosarcoma; malignant melanoma; amelanotic melanoma; superficial spreading melanoma; malignant melanoma in giant pigmented nevus; epithelioid cell melanoma; blue nevus, malignant; sarcoma; fibrosarcoma; fibrous histiocytoma, malignant; myxosarcoma; liposarcoma; leiomyosarcoma; rhabdomyosarcoma; embryonal rhabdomyosarcoma; alveolar rhabdomyosarcoma; stromal sarcoma; mixed tumor, malignant; mullerian mixed tumor; nephroblastoma; hepatoblastoma; carcinosarcoma; mesenchymoma, malignant; brenner tumor, malignant; phyllodes tumor, malignant; synovial sarcoma; mesothelioma, malignant; dysgerminoma; embryonal carcinoma; teratoma, malignant; struma ovarii, malignant; choriocarcinoma; mesonephroma, malignant; hemangiosarcoma; hemangioendothelioma, malignant; kaposi's sarcoma; hemangiopericytoma, malignant; lymphangiosarcoma; osteosarcoma; juxtacortical osteosarcoma; chondrosarcoma; chondroblastoma, malignant; mesenchymal chondrosarcoma; giant cell tumor of bone; ewing's sarcoma; odontogenic tumor, malignant; ameloblastic odontosarcoma; ameloblastoma, malignant; ameloblastic fibrosarcoma; pinealoma, malignant; chordoma; glioma, malignant; ependymoma; astrocytoma; protoplasmic astrocytoma; fibrillary astrocytoma; astroblastoma; glioblastoma; oligodendroglioma; oligodendroblastoma; primitive neuroectodermal; cerebellar sarcoma; ganglioneuroblastoma; neuroblastoma; retinoblastoma; olfactory neurogenic tumor; meningioma, malignant; neurofibrosarcoma; neurilemmoma, malignant; granular cell tumor, malignant; malignant lymphoma; hodgkin's disease; hodgkin's; paragranuloma; malignant lymphoma, small lymphocytic; malignant lymphoma, large cell, diffuse; malignant lymphoma, follicular; mycosis fungoides; other specified non-hodgkin's lymphomas; malignant histiocytosis; multiple myeloma; mast cell sarcoma; immunoproliferative small intestinal disease; leukemia; lymphoid leukemia; plasma cell leukemia; erythroleukemia; lymphosarcoma cell leukemia; myeloid leukemia; basophilic leukemia; eosinophilic leukemia; monocytic leukemia; mast cell leukemia; megakaryoblastic leukemia; myeloid sarcoma; and hairy cell leukemia. Nonetheless, it is also recognized that the present invention may also be used to treat a non-cancerous disease (e.g., a fungal infection, a bacterial infection, a viral infection, and/or a neurodegenerative disease).

C. AIDS or HIV-1 Infection

According to an embodiment of the invention, the methods described herein are useful in inhibiting the development of and/or treating AIDS or HIV-1 infections. In a specific embodiment, treatment is by inhibiting or reducing the expression of DUX4-fl or DEFB103A/B.

In accordance with another embodiment, the methods of this invention can be applied in conjunction with, or supplementary to, the customary treatments of AIDS or HIV-1 infection. Historically, the recognized treatment for HIV-1 infection is nucleoside analogs, inhibitors of HIV-1 reverse transcriptase (RT). Intervention with these antiretroviral agents has led to a decline in the number of reported AIDS cases and has been shown to decrease morbidity and mortality associated with advanced AIDS. Prolonged treatment with these reverse transcriptase inhibitors eventually leads to the emergence of viral strains resistant to their antiviral effects. Recently, inhibitors of HIV-1 protease have emerged as a new class of HIV-1 chemotherapy. HIV-1 protease is an essential enzyme for viral infectivity and replication. Protease inhibitors have exhibited greater potency against HIV-1 in vitro than nucleoside analogs targeting HIV-1 RT. Inhibition of HIV-1 protease disrupts the creation of mature, infectious virus particles from chronically infected cells. This enzyme has become a viable target for therapeutic intervention and a candidate for combination therapy.

D. Transplant/Graft Rejection

The success of surgical transplantation of organs and tissue is largely dependent on the ability of the clinician to modulate the immune response of the transplant recipient. Specifically the immunological response directed against the transplanted foreign tissue must be controlled if the tissue is to survive and function. Currently, skin, kidney, liver, pancreas, lung and heart are the major organs or tissues with which allogeneic transplantations are performed. It has long been known that the normally functioning immune system of the transplant recipient recognizes the transplanted organ as “non-self” tissue and thereafter mounts an immune response to the presence of the transplanted organ. Left unchecked, the immune response will generate a plurality of cells and proteins that will ultimately result in the loss of biological functioning or the death of the transplanted organ.

This tissue/organ rejection can be categorized into three types: hyperacute, acute and chronic. Hyperacute rejection is essentially caused by circulating antibodies in the blood that are directed against the tissue of the transplanted organ (transplant). Hyperacute rejection can occur in a very short time—often in minutes—and leads to necrosis of the transplant. Acute graft rejection reaction is also immunologically mediated and somewhat delayed compared to hyperacute rejection. The chronic form of graft rejection that can occur years after the transplant is the result of a disease state commonly referred to as Graft Arterial Disease (GAD). GAD is largely a vascular disease characterized by neointimal proliferation of smooth muscle cells and mononuclear infiltrates in large and small vessels. This neointimal growth can lead to vessel fibrosis and occlusion, lessening blood flow to the graft tissue and resulting in organ failure. Current immunosuppressant therapies do not adequately prevent chronic rejection. Most of the gains in survival in the last decade are due to improvements in immunosuppressive drugs that prevent acute rejection. However, chronic rejection losses remain the same and drugs that can prevent it are a critical unmet medical need.

According to an embodiment of the invention, the methods described herein are useful in inhibiting innate immune response in cell graft or tissue graft rejection. Thus, the methods are useful for such grafted tissue as heart, lung, kidney, skin, cornea, liver, neuronal tissue or cell, or with stem cells, including hematopoetic or embryonic stem cells. In accordance herewith, treatment can be by inducing or increasing the expression or activity of DUX4-fl or its target genes such as DEFB103.

In accordance with another embodiment, the methods of this invention can be applied in conjunction with, or supplementary to, the customary treatments of transplant/graft rejection. Tissue graft and organ transplant recipients are customarily treated with one or more cytotoxic agents in an effort to suppress the transplant recipient's immune response against the transplanted organ or tissue. Current immunosuppressant drugs include: cyclosporin, tacrolimus (FK506), sirolimus (rapamycin), methotrexate, mycophenolic acid (mycophenolate mofetil), everolimus, azathiprine, steroids and NOX-100. All of these drugs have side effects (detailed below) that complicate their long-term use. For example, cyclosporin (cyclosporin A), a cyclic polypeptide consisting of 11 amino acid residues and produced by the fungus species Tolypocladium inflatum Gams, is currently the drug of choice for administration to the recipients of allogeneic kidney, liver, pancreas and heart (i.e., wherein donor and recipient are of the same species of mammals) transplants. However, administration of cyclosporin is not without drawbacks as the drug can cause kidney and liver toxicity as well as hypertension. Moreover, use of cyclosporin can lead to malignancies (such as lymphoma) as well as opportunistic infection due to the “global” nature of the immunosuppression it induces in patients receiving long term treatment with the drug, i.e., the hosts normal protective immune response to pathogenic microorganisms is down-regulated thereby increasing the risk of infections caused by these agents. FK506 (tacrolimus) has also been employed as an immunosuppressive agent as a stand-alone treatment or in combination. Although its immunosuppressive activity is 10 100 times greater than cyclosporin, it still has toxicity issues. Known side effects include kidney damage, seizures, tremors, high blood pressure, diabetes, high blood potassium, headache, insomnia, confusion, seizures, neuropathy, and gout. It has also been associated with miscarriages. Methotrexate is commonly added to the treatment of the cytotoxic agent. Methotrexate is given in small doses several times after the transplant. Although the combination of cyclosporin and methotrexate has been found to be effective in decreasing the severity of transplant rejection, there are side effects, such as mouth sores and liver damage. Severe transplant rejection can be treated with steroids. However, the side effects of steroids can be extreme, such as weight gain, fluid retention, elevated blood sugar, mood swings, and/or confused thinking.

E. Autoimmune Disease

“Autoimmune Disease” refers to those diseases which are commonly associated with the nonanaphylactic hypersensitivity reactions (Type II, Type III and/or Type IV hypersensitivity reactions) that generally result as a consequence of the subject's own humoral and/or cell-mediated immune response to one or more immunogenic substances of endogenous and/or exogenous origin. Such autoimmune diseases are distinguished from diseases associated with the anaphylactic (Type I or IgE-mediated) hypersensitivity reactions.

According to an embodiment of the invention, the methods described herein are useful in inhibiting the development of an autoimmune disease comprising inducing or increasing the expression or activity of DUX4-fl or its target genes such as DEFB103 in a subject.

Thus, the methods are useful for such autoimmune diseases as multiple sclerosis, systemic lupus erythematosus, type 1 diabetes, viral endocarditis, viral encephalitis, rheumatoid arthritis, Graves' disease, autoimmune thyroiditis, autoimmune myositis, and discoid lupus erythematosus.

The methods in accordance with this aspect of the invention may also comprise positive modulation of DUX4 or its target gene such as DEFB103A or DEFB103B. In certain aspect, if the subject has a disease such as an autoimmune disease that are caused by the misexpression of DUX4 (as determined by a higher level or activity than a normal control), such as FSHD, methods involving inhibiting expression or activity of DUX4 or its target genes (such as the DEFB103A or DEFB103 or cancer testis antigens) may applied to the subject for treatment.

XII. KITS

Certain aspects of the present invention provide kits, such as diagnostic and therapeutic kits, as well as kits for preparing and/or screening antibodies. For example, a kit may comprise one or more pharmaceutical compositions as described herein and optionally instructions for their use. Kits may also comprise one or more devices for accomplishing administration of such compositions. For example, a subject kit may comprise a pharmaceutical composition and catheter for accomplishing direct intraarterial injection of the composition into a cancerous tumor. In other embodiments, a subject kit may comprise pre-filled ampoules of a protein isoform specific antibody construct, optionally formulated as a pharmaceutical, or lyophilized, for use with a delivery device.

Kits may comprise a container with a label. Suitable containers include, for example, bottles, vials, and test tubes. The containers may be formed from a variety of materials such as glass or plastic. The container may hold a composition which includes an antibody that is effective for therapeutic or non-therapeutic applications, such as described above. The label on the container may indicate that the composition is used for a specific therapy or non-therapeutic application, and may also indicate directions for either in vivo or in vitro use, such as those described above. The kit of the invention will typically comprise the container described above and one or more other containers comprising materials desirable from a commercial and user standpoint, including buffers, diluents, filters, needles, syringes, and package inserts with instructions for use.

XIII. EXAMPLES

The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

Example 1

This Example demonstrates that DUX4-fl activates the expression of germline genes and binds uniformly throughout the genome.

Background/Rationale:

Previously, the inventors identified two different DUX4 mRNA transcripts in human skeletal muscle, both at extremely low abundance: a full-length open reading frame mRNA (DUX4-fl) only detected in FSHD muscle and an internally spliced form of DUX4 mRNA (DUX4-s) that maintains the N-terminal double-homeobox domains but deletes the C-terminal domain and is detected in both control and FSHD muscle (Snider et al., 2010). Forced over-expression of DUX4-fl is toxic to cells, inducing apoptotic cell death (Kowaljow et al., 2007; Wallace et al., 2011), whereas forced over-expression of DUX4-s is not toxic to cultured human skeletal muscle cells (Geng et al., 2011).

To determine whether gene expression is regulated by DUX4-fl and/or DUX4-s in human muscle cells, as described in this Example, the inventors transduced primary myoblasts from a control individual (unaffected by muscle disease) with a lentiviral vector expressing either DUX4-fl or DUX4-s and performed expression microarrays.

Methods and Materials:

Transduction of Primary Control Myoblasts with Lentiviral Vectors Expressing DUX4 fl or DUX4-s

Lentiviral vectors expressing either DUX4-fl or DUX4-s were constructed as follows:

The DUX4-fl and DUX4-s lentiviral constructs were generated by replacing the GFP gene in the lentiviral vector backbone “pRRLSIN.cPPT.PGK-GPF.WPRE”, as described in http://www.addgene.org/12252/” incorporated herein by reference, with the cDNA encoding DUX-4fl (SEQ ID NO:108 or SEQ ID NO:109), or with the cDNA encoding DUX4-s (SEQ ID NO:111).

Primary myoblasts from a control individual unaffected by muscle disease were transduced with the Lentiviral vectors expressing either DUX4-fl or DUX4-s. Primary human myoblasts were collected and cultured as previously described (Snider et al., 2010). Primary myoblasts were maintained at or below 70% confluency for proliferation. For differentiation, cells were allowed to reach 95-100% confluency in growth medium. Once confluency was reached, the cells were changed to differentiation medium (F10 media supplemented with 1% horse serum, 10 μg/mL insulin, and 10 μg/mL transferrin, penicillin/streptomycin) and maintained for 4 days. Human RD cells were grown in DMEM in 10% bovine calf serum (Hyclone) and penicillin/streptomycin. The primary myoblasts were transduced with lentivirus carrying DUX-fl, DUX4- or GFP (MOI=15).

Expression Analysis

Expression microarrays were performed on the transduced cells at 24 hours after transduction as follows. Quadruplicate total RNA samples were collected from control human primary myoblasts transduced with lentivirus carrying DUX4-fl, DUX4-s or GFP (MOI=15) for 24 h. Samples were analyzed by Illumina Human Whole Genome microarrays. Probe intensities were corrected, normalized, and summarized by the Lumi package of Bioconductor (Du et al., 2008). Differentially expressed genes were identified by the LIMMA package of Bioconductor (Wettenhall and Smyth, 2004). Gene set enrichment analysis (GSEA) was performed using the Bioconductor GOstats package (Falcon and Gentleman, 2007).

Microarray Gene Target Validation by RT-PCR

RNA was collected from cultured control skeletal muscle either transduced with a DUX4-fl expressing lentivirus (+) or not transduced (−). RPL13A was used as an internal standard. Total RNA was treated with DNase using TURBO DNA-free kit (Ambion) according to manufacturer's protocol. One μg of DNase-treated RNA was reverse transcribed to first strand cDNA with SuperScript III and anchored oligo dT (Invitrogen) at 52° C. for 1 h. Residual RNA was digested with RNase H at 37° C. for 20 min. cDNA was used in various PCR and real-time PCR reactions with primers listed below.

cDNA from DUX4-fl transduced or untransduced primary myoblasts was diluted 1:5 and used in PCR reactions with Platinum Taq polymerase (Invitrogen) with conditions of 55° C. annealing temperature and 35 cycles. The primers shown below were designed to span exon-exon junctions where possible. Primers from select genes were also used in real-time PCR reactions to examine endogenous expression of targets in FSHD versus control samples described separately.

Gene Forward primer Reverse primer name sequence sequence TRIM43 ACCCATCACTGGACTGGTGT CACATCCTCAAAGAGCCTGA (SEQ ID NO: 113) (SEQ ID NO: 114) PRAMEF1 GCTGGAACACCTTCAGTTGC AGTTCTCCAAGGGGTTCTGG (SEQ ID NO: 115) (SEQ ID NO: 116) RFPL4B GAGACGTAGGCTTCGGATCTT GGCTGAATTCAAGTGGGTCT (SEQ ID NO: 117) (SEQ ID NO: 118) ZSCAN4 TGGAAATCAAGTGGCAAAAA CTGCATGTGGACGTGGAC (SEQ ID NO: 119) (SEQ ID NO: 120) KHDC1 ACCAATGGTGTTTCACATGG TGAATAAGGGTGTGGCTGTG (SEQ ID NO: 121) (SEQ ID NO: 122) RFPL2 CCCACATCAAGGAACTGGAG TGTTGGCATCCAAGGTCATA (SEQ ID NO: 123) (SEQ ID NO: 124) CXCR4 CGTGGAACGTTTTTCCTGTT GGTGCTGAAATCAACCCACT (SEQ ID NO: 125) (SEQ ID NO: 126) WDR33 GGTCCCACCTATAGGAATGT GACCAAGCGTCTTCCTTCTG TG (SEQ ID NO: 128) (SEQ ID NO: 127) MBD3L2 GCGTTCACCTCTTTTCCAAG GCCATGTGGATTTCTCGTTT (SEQ ID NO: 129) (SEQ ID NO: 130) CCNA1 TGAAGCAGATCCATTCTTGA ACCCTGTAAATGCAGCAAGG AA (SEQ ID NO: 132) (SEQ ID NO: 131) TRIM48 TGAATGTGGAAACCACCAGA GTTGAGCCTGTCCCTCAGTC (SEQ ID NO: 133) (SEQ ID NO: 134) PRAMEF2 ACCTTCTTCAGTGGGCACCT TGGGAACTGGGAGAGACACT (SEQ ID NO: 135) (SEQ ID NO: 136) IFI27 CCATAGCAGCCAAGATGATG GAACTTGGTCAATCCGGAGA (SEQ ID NO: 137) (SEQ ID NO: 138) TESK2 GCAGGAGAGGGATAGGAAGC CTTGTGGGGGATCTTGTCAT (SEQ ID NO: 139) (SEQ ID NO: 140) PELI1 CTAAGGCAAATGGGGTGAAG TCTGGGCCCGAGATAAAGTA (SEQ ID NO: 141) (SEQ ID NO: 142) FRG2B GTCCAGCTCATATCGGGAAA GCTGCACTCCTTTTCTGGAC (SEQ ID NO: 143) (SEQ ID NO: 144) HSPA2 CTTCTGCCGTGATTGTGAGG CCAGGGGGTCTAGGTAGGAG (SEQ ID NO: 145) (SEQ ID NO: 146) RPL13A AACCTCCTCCTTTTCCAAGC GCAGTACCTGTTTAGCCACGA (SEQ ID NO: 147) (SEQ ID NO: 148)

Results: Identification of Genes Regulated by DUX4 in Human Primary Myoblasts

At 24 hours after transduction, DUX4-fl increased the expression of 1071 genes and decreased the expression of 837 genes compared to a control myoblast population similarly infected with a GFP expressing lentivirus (2-fold change and FDR<0.01); whereas DUX4-s increased the expression of 159 genes and decreased expression of 45 genes. The full set of genes regulated by DUX4-fl or DUX4-s is in Table 1, provided in the appendix.

Table 1 (included as an Appendix) shows the expression array analysis of DUX4-fl and DUX4-s in cultured human skeletal muscle.

Using a more stringent 3-fold criteria (>1.584 log₂-fold change and FDR<0.01), 466 genes were increased and 244 decreased by DUX4-fl; and 37 were increased and one decreased by DUX4-s. Only two annotated genes were increased 3-fold or more by both (CCNA1, MAP2), and none were decreased 3-fold or more by both.

In view of the fact that Table 1 lists the fold-change in log 2, a value of “3” in Table 1 would be an 8-fold change. As shown in Table 1, 164 genes were identified that increase 8-fold or more, 107 increased 16-fold or more, and 72 genes increased 32-fold or more (i.e. log 2fc≧5).

The 107 genes that were found to be increased by at least 16-fold or greater in the presence of DUX4-fl are useful as FSHD biomarkers and are provided below in Table 2:

TABLE 2 FSHD Biomarker Genes upregulated by DUX4-fl SEQ ID NO: Symbol RefSeq* full_fc full_pval 1 RFPL1S NR_002727.1 8.395820858 4.68E−27 2 LOC643263 XR_016355.1 8.345299826 5.16E−27 3 RFPL4B NM_001013734.2 8.340345819 5.13E−28 4 LOC390031 XM_372343.1 8.330613566 5.02E−28 5 ZSCAN4 NM_152677.1 8.321990102 1.94E−28 6 LOC340970 XR_038494.1 8.315993278 3.20E−28 7 LOC136157 XM_069743.3 8.298510216 1.98E−27 8 LOC643445 XR_038080.1 8.249957558 1.44E−28 9 LOC729458 XM_001130308.2 8.246687197 2.30E−27 10 LOC653192 XM_926437.2 8.228018909 2.48E−27 11 LOC645669 XM_928680.1 8.202022481 1.85E−27 12 LOC391769 XM_001713901.1 8.189552468 3.39E−27 13 LOC196120 XM_114987.3 8.178925427 2.42E−27 14 LOC651308 XM_940443.1 8.168661444 4.84E−25 15 RFPL3 NM_001098535.1 8.144474769 9.29E−29 16 PRAMEF1 NM_023013.1 8.072400408 3.19E−27 17 LOC100134199 XM_001719549.1 8.048036849 6.76E−28 18 SPRYD5 NM_032681.1 8.044967325 5.44E−28 19 LOC284428 XM_208203.5 8.022522551 1.38E−26 20 LOC642362 XM_925891.1 8.015825025 1.66E−27 21 KHDC1L NM_001126063.2 8.012411091 1.06E−27 22 LOC653656 XM_928688.3 7.897231482 5.40E−28 23 TRIM48 NM_024114.2 7.880137061 5.54E−26 24 LOC653657 XM_928697.2 7.856575803 3.03E−27 25 PRAMEF12 NM_001080830.1 7.801903788 1.84E−25 26 LOC441584 XM_497258.1 7.781378819 4.75E−27 27 LOC730974 XR_037751.1 7.715075519 9.06E−26 28 PRAMEF7 NM_001012277.1 7.631155888 1.22E−27 29 MBD3L2 NM_144614.2 7.622770725 3.46E−26 30 LOC440040 XM_495873.4 7.533852122 2.79E−27 31 CCNA1 NM_003914.2 7.525825564 1.10E−26 32 PRAMEF13 XM_001713933.1 7.421574077 3.37E−27 33 LOC342900 XM_001129035.1 7.391093477 4.53E−28 34 LOC340096 XM_293943.2 7.38245832 9.80E−25 35 PRAMEF5 NM_001013407.1 7.34950535 3.80E−23 36 RFPL2 NM_006605.1 7.293384138 3.38E−25 37 PRAMEF9 NM_001010890.1 7.130773908 7.31E−25 38 LOC100134006 XM_001725030.1 7.08721139 7.77E−27 39 PRAMEF4 NM_001009611.1 7.060257208 2.65E−24 40 PRAMEF15 XM_001713659.1 7.000221925 4.98E−26 41 LOC100131392 XM_001713681.1 6.975776511 9.12E−25 42 NP NM_000270.1 6.960976026 4.12E−27 43 LOC399939 XM_374919.3 6.930795087 9.92E−27 44 LOC642148 XR_019607.1 6.85089804 8.92E−25 45 LOC729384 NM_001105522.1 6.831960625 2.20E−27 46 ZNF705A NM_001004328.1 6.831813353 3.44E−27 47 C6orf148 NM_030568.2 6.759160491 7.93E−25 48 TRIM49 NM_020358.2 6.551062725 3.44E−26 49 DEFB103A NM_001081551.2 6.441860402 1.15E−25 50 PRAMEF2 NM_023014.1 6.439143984 2.12E−25 51 RFPL1 NM_021026.2 6.264001827 8.17E−25 52 LOC100133984 XM_001723079.1 6.203778673 8.08E−25 53 LOC642127 XM_936272.2 6.112037689 6.46E−24 54 CA2 NM_000067.1 6.091135387 5.91E−24 55 PRAMEF10 NM_001039361.1 6.063554254 1.77E−23 56 LOC646698 XM_929644.2 6.012022368 9.84E−24 57 LOC729516 XR_038445.1 5.954919316 1.03E−25 58 PRAMEF11 XM_001714028.1 5.93984508 1.97E−24 59 CSAG3 NM_001129826.1 5.871224381 6.50E−24 60 PRAMEF6 NM_001010889.2 5.82553958 8.31E−25 61 LOC391764 XM_373076.3 5.820931052 1.05E−24 62 TRIM43 NM_138800.1 5.805862854 1.43E−20 63 LOC391742 XM_373056.1 5.733140049 1.50E−25 64 LOC391766 XM_373077.2 5.723821554 3.38E−25 65 ZNF296 NM_145288.1 5.536035027 9.82E−25 66 SLC34A2 NM_006424.2 5.513611409 5.77E−22 67 LOC391767 XM_373078.1 5.491772222 3.46E−21 68 LOC729368 XM_001130065.2 5.416246795 1.19E−23 69 LOC440563 NM_001136561.1 5.312436177 3.77E−22 70 LOC646754 XM_929704.2 5.110280465 3.49E−22 71 LOC654101 XM_939354.1 5.033863949 5.71E−21 72 LOC729731 XM_001131140.1 5.007248294 1.46E−23 73 HIST2H3A NM_001005464.2 4.94502277 2.03E−21 74 TRIM64 XM_061890.11 4.943161345 2.26E−23 75 LOC402207 XM_377884.2 4.902732221 6.85E−23 76 LOC729700 XM_001131081.1 4.817203 1.04E−23 77 LOC645558 XM_928577.2 4.802893 1.18E−22 78 LOC642219 XM_936370.2 4.798732 2.95E−20 79 PRAMEF20 NM_001099852.1 4.795166 1.03E−23 80 HBA1 NM_000558.3 4.786546 5.55E−23 81 TRIM53 XR_041244.1 4.777538 1.16E−22 82 LOC399940 NM_001136118.1 4.726731 6.54E−22 83 HBA2 NM_000517.3 4.72082 4.76E−24 84 LOC646103 XM_377879.3 4.658033 6.41E−21 85 LOC732393 XR_015873.1 4.637178 1.36E−21 86 LOC100133446 XM_001717965.1 4.634629 4.84E−23 87 LOC100131539 XM_001724873.1 4.629059 6.67E−21 88 C12orf50 NM_152589.1 4.521768 6.50E−23 89 OR2T34 NM_001001821.1 4.519029 5.05E−23 90 TPRX1 NM_198479.2 4.48321 1.10E−23 91 LOC402199 XM_377875.2 4.39249 3.01E−21 92 LOC646066 XM_116384.2 4.391241 2.75E−21 93 ART3 NM_001179.3 4.363323 2.34E−22 94 RFPL4A XM_001719234.1 4.347532 6.99E−22 95 LOC401860 XM_377445.3 4.272237 3.19E−21 96 NXF1 NM_006362.4 4.233044 3.92E−22 97 LOC729706 XM_001131091.1 4.227191 1.26E−21 98 PRAMEF17 XM_938420.2 4.223086 5.13E−20 99 SFRS2B NM_032102.2 4.215303 3.27E−22 100 RN5S9 NR_023371.1 4.191231 9.29E−23 101 PPP2R2B NM_181677.1 4.130028 1.09E−21 102 ZNF217 NM_006526.2 4.113561 6.85E−22 103 ENTPD8 NM_001033113.1 4.072927 1.36E−21 104 LOC647827 XR_018213.1 4.053399 4.92E−20 105 THOC4 XM_001134346.1 4.034801 7.79E−22 106 LOC729694 XM_001131061.1 4.028728 2.38E−19 107 DEFB103BA NM_018661.3 *Genbank reference No. as accessed on Jul. 22, 2011.

A representative sample of genes activated by DUX4-fl is shown in Table 3.

TABLE 3 Representative genes induced by DUX4-fl Log₂ Log₂ DUX4-fl DUX4-s Category Fc* Fc* Comments Germline and Stem Cells ZSCAN4 8.3 0.0 Genome stability, telomere length (SEQ ID NO: 5) PRAMEF1 8.1 0.1 Melanoma antigen family (SEQ ID NO: 16) SPRYD5 8.0 −0.1 Expressed in oocyte (SEQ ID NO: 18) KHDC1L (SEQ 8.0 −0.1 KH RNA binding domain ID NO: 21) MBD3L2 (SEQ 7.6 0.0 Methyl-CpG-binding protein ID NO: 29) ZNF705A 6.8 −0.1 Zinc finger protein (SEQ ID NO: 46) TRIM43 5.8 0.0 Preimplantation embryo (SEQ ID NO: 62) TPRX1 4.5 −0.1 Homeobox protein (SEQ ID NO: 90) ZNF217 4.1 −0.3 Expressed in cancer stem cells (SEQ ID No: 102) HSPA2 3.7 −0.3 Chaperone, heat shock 70 kd JUP 3.2 −0.1 expressed in germline and testicular cancers FGFR3 3.1 0.0 Expressed in spermatogonia CD24 2.6 −0.4 Stem cell marker SLC2A14 2.4 0.2 Spermatogenesis ID2 2.3 0.3 Negative regulator of cell differentiation PVRL3 2.2 0.4 Spermatid-sertoli junction HOXB2 2.2 0.0 Anterior-posterior axis development ZSCAN2 2.2 −0.2 Spermatogenesis and embryonic development RNA Processing SFRS2B (SEQ 4.2 −0.3 Splicing ID NO: 99) THOC4 4.0 −0.2 Splicing, RNA transport (SEQ ID NO: 105) ZNHIT6 3.5 0.3 sno-RNA processing DBR1 3.4 0.2 RNA lariat debranching enzyme TFIP11 3.2 0.1 Splicesome assembly CWC15 2.6 0.1 Spliceosome-associated ARS2 2.6 −0.2 miRNA processing PABPN1 2.6 −0.3 PolyA binding SFRS17A 2.5 0.2 Spliceosome-associated RMRP 2.3 0.1 Mitochondrial RNA processing SNIP1 2.1 −0.2 miRNA biogenesis RPPH1 2.0 0.2 tRNA processing RNGTT 2.0 −0.6 mRNA processing Ubiquitin Pathway SIAH1 3.7 −0.1 Targets TRF2 telomere maintenance FBXO33 3.2 0.2 E3 ubiquitin-protein ligase complex PELI1 2.9 0.1 E3 ligases involved in innate immunity USP29 2.6 −0.1 Ubiquitin-specific peptidase ARIH1 2.2 0.8 Ubiquitin-conjugating enzyme E2 binding protein TRIM23 2.2 0.6 E3 ubiquitin ligase involved in immunity Immunity and Innate Defense DEFB103B 6.4 0.1 Innate defense (SEQ ID NO: 49) IFRD1 3.0 −0.2 Interferon-related developmental regulator CXADR 2.5 −0.1 Leukocyte migration CBARA1 2.1 −0.2 T-helper 1-mediated autoreactivity SON 2.1 −0.3 Viral response CXCR4 2.0 −0.1 Chemotaxis General Transcription GTF2F1 3.2 0.3 General transcription factor IIF MED26 2.1 0.1 RNA Pol II mediator complex RRN3 2.1 0.1 RNA Pol I preinitiation complex Cancer Expressed CSAG3 5.9 0.1 Chondrosarcoma-associated gene (SEQ ID NO: 59) SLC34A2 5.5 0.0 Breast cancer biomarker (SEQ ID NO: 66) PNMA6B 3.6 −0.2 Paraneoplastic antigen CSE1L 2.9 0.1 Cellular apoptosis susceptibility protein AMACR 2.7 0.1 Prostate cancer biomarker Other FLJ45337 3.7 −0.2 Endogenous retrovirus HNRNPCL1 3.5 −0.1 Nucleosome assembly SPTY2D1 3.3 −0.3 Suppressor of ty retrotransposons in yeast MGC10997 2.4 −0.3 Endogenous retrotransposon

The Gene Ontology (GO) terms significantly enriched in 3-fold up-regulated genes by DUX4-fl included categories such as RNA polymerase II mediator complexes, RNA splicing and processing, and gamete/spermatogenesis, as shown in Table 4.

Table 4 shows the gene Ontology analysis of genes up-regulated by DUX4-fl.

TABLE 4 Gene Ontology Analysis of genes upregulated by DUX4-fl GOID Pvalue OddsRatio ExpCount Count Size Term Ontology Geneset GO: 0016455 0.000191764 11.43687515 0.561257787 5 22 RNA polymerase II transcription MF fc3.up mediator activity GO: 0016592 0.000328786 9.937015504 0.623932435 5 25 mediator complex CC fc3.up GO: 0016607 3.11E−07 6.292245907 2.620516227 14 105 nuclear speck CC fc3.up GO: 0000398 0.000279448 6.248262359 1.294881345 7 52 nuclear mRNA splicing, via spliceosome BP fc3.up GO: 0007411 0.004634577 5.074925075 1.10245249 5 44 axon guidance BP fc3.up GO: 0003729 0.005361849 4.884960159 1.140029688 5 45 mRNA binding MF fc3.up GO: 0006986 0.002679577 4.752207792 1.406677266 6 56 response to unfolded protein BP fc3.up GO: 0005681 2.10E−05 4.514666667 3.244448662 13 130 spliceosomal complex CC fc3.up GO: 0000375 0.000181802 4.508736326 2.486804452 10 99 RNA splicing, via transesterification BP fc3.up reactions GO: 0048762 0.007434327 4.483738245 1.230842607 5 49 mesenchymal cell differentiation BP fc3.up GO: 0050657 0.000411547 4.442982456 2.26073132 9 90 nucleic acid transport BP fc3.up GO: 0051236 0.000411547 4.442982456 2.26073132 9 90 establishment of RNA localization BP fc3.up GO: 0008380 4.17E−05 3.948955478 3.96665952 14 163 RNA splicing BP fc3.up GO: 0019222 0.022673693 3.317567568 1.622481442 5 70 regulation of metabolic process BP fc3.up GO: 0010720 0.023351201 3.282327586 1.632750397 5 65 positive regulation of cell development BP fc3.up GO: 0006397 0.001604973 2.933267749 4.427103404 12 183 mRNA processing BP fc3.up GO: 0010769 0.038069546 2.851386807 1.858823529 5 74 regulation of cell morphogenesis involved BP fc3.up in differentiation GO: 0051169 0.00252323 2.765977011 4.67217806 12 186 nuclear transport BP fc3.up GO: 0001655 0.043864833 2.734187109 1.93257471 5 77 urogenital system development BP fc3.up GO: 0007018 0.043997794 2.731681034 1.93418124 5 77 microtubule-based movement BP fc3.up GO: 0002521 0.027827111 2.514466403 2.938950715 7 117 leukocyte differentiation BP fc3.up GO: 0007275 0.021259682 2.127133015 5.476301779 11 233 multicellular organismal development BP fc3.up GO: 0044419 0.013115877 2.123638693 6.473314905 13 258 interspecies interaction between BP fc3.up organisms GO: 0007276 0.046093024 2.102561097 3.977549711 8 159 gamete generation BP fc3.up GO: 0005654 0.011464976 2.095199054 7.064796326 14 309 nucleoplasm CC fc3.up GO: 0007283 0.042362233 2.035263158 4.621939587 9 184 spermatogenesis BP fc3.up GO: 0006915 0.038108478 1.992664746 5.256515307 10 209 apoptosis BP fc3.up GO: 0070013 3.55E−05 1.856371356 40.15629152 65 1609 intracellular organelle lumen CC fc3.up GO: 0032504 0.028221469 1.849315475 7.937678855 14 316 multicellular organism reproduction BP fc3.up GO: 0031974 8.33E−05 1.794502609 41.2793699 65 1654 membrane-enclosed lumen CC fc3.up GO: 2000026 0.045419104 1.721140016 8.484942332 14 341 regulation of multicellular organismal BP fc3.up development GO: 0005634 2.40E−05 1.680057275 99.52516619 132 4000 nucleus CC fc3.up GO: 0003723 0.026131966 1.675158085 12.53272055 20 512 RNA binding MF fc3.up GO: 0050794 0.003573262 1.663024053 31.57386454 46 1223 regulation of cellular process BP fc3.up GO: 0005730 0.018174998 1.641408991 16.04754223 25 643 nucleolus CC fc3.up GO: 0060255 0.00375921 1.575747148 38.14639346 54 1498 regulation of macromolecule metabolic BP fc3.up process GO: 0034641 0.001043025 1.543947976 72.70723982 95 2819 cellular nitrogen compound metabolic BP fc3.up process GOID: Gene Ontology ID ExpCount: expected count Count: actual count in data set Size: size of GO term Term: GO term Geneset: genes upregulated by DUX4-fl by 3x fold change or more

The down-regulated genes represent the immune response pathways, as shown in TABLE 5.

Table 5 shows the Gene Ontology analysis of genes down-regulated by DUX4-fl.

TABLE 5 Gene Ontology Analysis of genes downregulated by DUX4-fl GOID Pvalue OddsRatio ExpCount Count Size Term Ontology Geneset GO: 0008009 4.46E−06 17.99454 0.461189 6 22 chemokine activity MF fc3.down GO: 0002253 3.77E−05 17.02899 0.40639 5 18 activation of immune response BP fc3.down GO: 0009615 9.02E−17 15.93194 1.893662 21 84 response to virus BP fc3.down GO: 0002541 8.86E−05 13.69643 0.478537 5 21 activation of plasma proteins involved in BP fc3.down acute inflammatory response GO: 0050792 0.000113 12.88936 0.501325 5 22 regulation of viral reproduction BP fc3.down GO: 0006955 2.35E−17 11.47143 3.073569 26 150 immune response BP fc3.down GO: 0045087 6.12E−09 10.07058 1.626719 13 73 innate immune response BP fc3.down GO: 0006952 0.000475 8.863863 0.664982 5 34 defense response BP fc3.down GO: 0050900 0.000804 7.869162 0.74721 5 33 leukocyte migration BP fc3.down GO: 0019882 0.000879 7.688316 0.761086 5 34 antigen processing and presentation BP fc3.down GO: 0048519 9.32E−06 7.615385 1.400399 9 68 negative regulation of biological process BP fc3.down GO: 0006959 0.000294 7.570055 0.93004 6 41 humoral immune response BP fc3.down GO: 0051384 0.000708 6.296703 1.089983 6 48 response to glucocorticoid stimulus BP fc3.down GO: 0042542 0.00279 5.753133 0.979862 5 43 response to hydrogen peroxide BP fc3.down GO: 0048545 0.004675 5.03714 1.101595 5 49 response to steroid hormone stimulus BP fc3.down GO: 0001664 0.000882 5.011867 1.551271 7 74 G-protein-coupled receptor binding MF fc3.down GO: 0060326 0.004951 4.965368 1.116587 5 49 cell chemotaxis BP fc3.down GO: 0006916 1.41E−05 4.709181 3.12766 13 140 anti-apoptosis BP fc3.down GO: 0023038 0.003257 4.534895 1.4584 6 64 signal initiation by diffusible mediator BP fc3.down GO: 0044419 7.31E−09 4.498795 6.540011 25 287 interspecies interaction between organisms BP fc3.down GO: 0050776 0.000861 4.411115 2.005544 8 90 regulation of immune response BP fc3.down GO: 0016757 0.008193 4.336898 1.254502 5 60 transferase activity, transferring MF fc3.down glycosyl groups GO: 0051604 0.001941 4.336606 1.777424 7 78 protein maturation BP fc3.down GO: 0032496 0.008947 4.250743 1.283484 5 57 response to lipopolysaccharide BP fc3.down GO: 0002684 7.38E−05 4.243549 3.160098 12 139 positive regulation of immune system BP fc3.down process GO: 0006935 0.010797 4.042572 1.34314 5 60 chemotaxis BP fc3.down GO: 0001871 0.004449 3.681051 2.054385 7 98 pattern binding MF fc3.down GO: 0006954 0.00274 3.618056 2.400128 8 111 inflammatory response BP fc3.down GO: 0005126 0.005119 3.579944 2.107496 7 101 cytokine receptor binding MF fc3.down GO: 0005615 4.47E−07 3.542467 8.041374 25 380 extracellular space CC fc3.down GO: 0009617 0.010017 3.519614 1.836402 6 81 response to bacterium BP fc3.down GO: 0007584 0.005785 3.50269 2.158862 7 95 response to nutrient BP fc3.down GO: 0030246 0.00614 3.452381 2.179423 7 105 carbohydrate binding MF fc3.down GO: 0009605 7.19E−05 3.377922 5.255012 16 239 response to external stimulus BP fc3.down GO: 0007568 0.007331 3.339047 2.255962 7 99 aging BP fc3.down GO: 0048584 0.004435 3.323799 2.596461 8 116 positive regulation of response to stimulus BP fc3.down GO: 0007626 0.001116 3.260458 3.668786 11 161 locomotory behavior BP fc3.down GO: 0051100 0.025205 3.204482 1.663487 5 73 negative regulation of binding BP fc3.down GO: 0008285 0.000348 3.167963 4.840465 14 216 negative regulation of cell proliferation BP fc3.down GO: 0031668 0.026548 3.157695 1.686275 5 74 cellular response to extracellular stimulus BP fc3.down GO: 0060548 5.55E−05 3.072478 6.859036 19 301 negative regulation of cell death BP fc3.down GO: 0007267 0.002407 2.9375 4.040065 11 179 cell-cell signaling BP fc3.down GO: 0007155 0.002567 2.911979 4.074034 11 182 cell adhesion BP fc3.down GO: 0008083 0.035758 2.892365 1.823791 5 87 growth factor activity MF fc3.down GO: 0002521 0.017372 2.78715 2.666137 7 117 leukocyte differentiation BP fc3.down GO: 0005625 0.002584 2.749994 4.676694 12 221 soluble fraction CC fc3.down GO: 0005576 1.10E−07 2.677219 19.78601 45 935 extracellular region CC fc3.down GO: 0002252 0.048324 2.650262 1.983392 5 90 immune effector process BP fc3.down GO: 0005792 0.017776 2.556128 3.301196 8 156 microsome CC fc3.down GO: 0090046 0.047437 2.399631 2.620562 6 115 regulation of transcription regulator activity BP fc3.down GO: 0060537 0.034573 2.390475 3.076312 7 135 muscle tissue development BP fc3.down GO: 0003714 0.049119 2.374029 2.641353 6 126 transcription corepressor activity MF fc3.down GO: 0040011 0.010723 2.363266 4.94011 11 218 locomotion BP fc3.down GO: 0080134 0.015205 2.237124 5.195548 11 228 regulation of response to stress BP fc3.down GO: 0010942 0.004177 2.182383 8.340223 17 366 positive regulation of cell death BP fc3.down GO: 0050896 0.00296 2.147643 10.29764 20 617 response to stimulus BP fc3.down GO: 0030154 0.006723 2.127693 8.050932 16 368 cell differentiation BP fc3.down GO: 0008233 0.014467 2.031607 7.274202 14 347 peptidase activity MF fc3.down GO: 0002520 0.029295 2.00897 5.742448 11 252 immune system development BP fc3.down GO: 0001568 0.038557 1.986315 5.263911 10 231 blood vessel development BP fc3.down GO: 0007165 0.010716 1.622598 21.94903 33 961 signal transduction BP fc3.down GOID: Gene Ontology ID ExpCount: expected count Count: actual count in data set Size: size of GO term Term: GO term Geneset: genes downregulated by DUX4-fl by 3x fold change or more

The up-regulation of a large number of transcription-related and RNA processing factors suggests that DUX4-fl might be a central component of a complex gene regulatory network, and the large number of germline associated genes suggests a possible role in reproductive biology.

In primary human myoblasts, DUX4-fl robustly induced a large number of genes not normally detected in skeletal muscle.

This set of DUX4-fl induced genes, especially ones such as the group of 107 genes (shown in TABLE 2) that were found to be increased by at least 16-fold or greater in the presence of DUX4-fl are useful as biomarkers of DUX4 activity in skeletal muscle, and therefore useful as biomarkers for the presence or risk of developing FSHD, since there would be extremely little to no background expression in control muscle.

GO analysis for these highly induced genes showed enrichment for gamete generation and spermatogenesis categories, as shown in TABLE 6.

TABLE 6 Gene Ontology Analysis of genes upregulated by DUX4-fl 8-fold or more GOID Pvalue OddsRatio ExpCount Count Size Term Ontology Geneset GO: 0042301 0.00082 58.85380117 0.0435084 2 11 phosphate binding MF fc8 GO: 0051327 0.019602 10.1148429 0.2166402 2 73 M phase of meiotic cell cycle BP fc8 GO: 0002521 0.046737 6.215384615 0.3472178 2 117 leukocyte differentiation BP fc8 GO: 0007283 0.016709 6.116685083 0.5460519 3 184 spermatogenesis BP fc8 GO: 0007276 0.033342 4.643037975 0.7122417 3 240 gamete generation BP fc8 GO: 0008270 9.41E−06 4.609476512 5.5730248 17 1409 zinc ion binding MF fc8 GO: 0002682 0.043192 4.1721673 0.7894012 3 266 regulation of immune system process BP fc8 GO: 0043167 7.01E−05 3.570087799 10.248195 22 2591 ion binding MF fc8 GOID: Gene Ontology ID ExpCount: expected count Count: actual count in data set Size: size of GO term Term: GO term Geneset: genes downregulated by DUX4-fl by 3x fold change or more

In many cases, DUX4-fl activated multiple members of gene families involved in germ cell biology and early development, including some primate-specific genes, as shown in Table 7.

TABLE 7 DUX4 highly activates gene families involved in germ cell and early development Gene Family Members Biological Context Fc range Preferentially PRAMEF1 Cancer-testis antigen  9-269 expressed in PRAMEF2 (Chang et al., 2011) melanoma family PRAMEF4-15 PRAMEF17 PRAMEF20 Tripartite TRIM43 Testis-expressed,  27-235 motif-containing TRIM48 preimplantation embryos TRIM49 (Stanghellini et al., 2009) TRIM53 TRIM64 Methyl-binding MBD3L2 Spermatids & germ cell 197-310 protein-like MBD3L3 tumors (Jiang et al., MBD3L5 2002; Jin et al., 2008) Zinc finger and ZSCAN4 Telomere maintenance in  13-320 SCAN domain ZSCAN5B embryonic stem cells containing ZSCAN5D (Zalzman et al., 2010) Ret-finger RFPL1 Primate neocortex  20-336 Protein-like RFPL1S development RFPL2 (Bonnefont, 2008) RFPL3 RFPL4A RFPL4B KH homology KHDC1 Oocyte- and embryo- 108-258 domain KHDC1L expressed containing (Pierre et al., 2007) Family with FAM90A1 Primate-specific gene  9-19 sequence FAM90A2P family with unknown similarity 90 FAM90A6P function FAM90A7 (Bosch et al., 2007)

The inventors validated the differential expression of 15 of the DUX4-fl regulated genes by RT-PCR, as shown in FIG. 1. FIG. 1 shows the results of RT-PCR validation of DUX-fl target genes shown to be upregulated in the expression microarray.

Discussion:

Prior genetic and molecular studies identified DUX4 as the most likely candidate gene for FSHD, however, the abundance of DUX4-fl mRNA was extremely low in FSHD muscle and the protein was not reliably detected. Therefore, it was unclear whether DUX4-fl was expressed at levels sufficient to have a biological consequence in FSHD. The inventors identified genes regulated by DUX4-fl and show that they are expressed at readily detectable levels in FSHD skeletal muscle, both cell lines and muscle biopsies, but not in control tissues, providing direct support for the model that misexpression of DUX4-fl is a causal factor for FSHD. Furthermore, the genes regulated by DUX4-fl suggest several specific mechanisms for FSHD pathophysiology and provide needed candidate biomarkers for the disease.

Currently, the diagnostic test for FSHD1 requires pulse-field gel electrophoresis and Southern blotting to detect the contraction of the D4Z4 repeats, and there are no commercially available diagnostic tests for FSHD2. The set of genes robustly upregulated by DUX4 in FSHD skeletal muscle are candidate biomarkers because they are easily detected in FSHD muscle but absent in control muscle. Furthermore, some target genes encode secreted proteins, such as CSE1L (SEQ ID NO:149) (Genbank NM_(—)177436.1 see Table 1), which suggests the potential for developing blood tests to diagnose FSHD or monitor response to interventions.

Many of the genes highly upregulated by DUX4-fl normally function in the germline and/or early stem cells and are not present in healthy adult skeletal muscle. This supports a biological role for DUX4-fl in germ cell development and suggests potential disease mechanisms for FSHD. Activation of the gametogenic program might be incompatible with post-mitotic skeletal muscle, leading to apoptosis or cellular dysfunction. Also, the testis is an immune-privileged site and testis proteins misexpressed in cancers can induce an immune response (Simpson et al., 2005). In fact, some of the genes regulated by DUX4-fl, such as the PRAME family (Chang et al., 2011), are known cancer testis antigens, so it is reasonable to suggest that expression of these genes in skeletal muscle might also induce an adaptive immune response. An immune-mediated mechanism for FSHD is consistent with the focal inflammation and CD8+ T cell infiltrates that characterize FSHD muscle biopsies (Frisullo et al., 2011; Molnar et al., 1991).

DUX4-fl regulated targets also include genes involved in RNA processing, developmentally regulated components of the PolII transcription complex, ubiquitin-mediated protein degradation pathways and the innate immune response pathways, all of which may have pathophysiological consequences. For example, abnormal splicing has been reported in FSHD, although this was attributed to potential misexpression of another candidate gene for FSHD, FRG1 (Gabellini et al., 2006). In addition, reactivation of retroelements can result in genomic instability (Belancio et al., 2010) and transcriptional deregulation (Schulz et al., 2006), so DUX4's activation of MaLR transcripts might contribute to the apoptosis or modulation of the innate immune response seen in muscle cells expressing DUX4.

Example 2

This Example describes the identification of DUX4-fl binding sites and a consensus binding sequence motif and demonstrates that DUX4-fl activates the expression of germline genes by binding to a double homeodomain motif.

Background/Rationale:

Double homeodomain proteins comprise a distinct group of DNA-binding proteins (Holland et al., 2007), but their consensus recognition sites and genomic targets are unknown. Therefore, the inventors performed chromatin immunoprecipitation combined with high throughput sequencing (ChIP-Seq) to identify DUX4-binding sites in human muscle cells, as described in this Example.

Methods: Antibody Development and Characterization

Custom anti-DUX4 polyclonal antibodies MO488 and MO489 were developed through Covance. Rabbits were immunogenized with GST-DUX4 C-terminus fusion protein as antigen (Geng et al., 2011). Human myoblasts were transduced with lentivirus-DUX4-fl and used for testing the antibodies on western blot and immunofluorescence as previously described in Geng et al., 2011, supra. Briefly described, for western blot, 5 μg of lysate from transfected or untransfected cells were run on 4-12% gradient bis-tris polyacrylamide gel and transferred to 0.45 μm nitrocellulose membranes. Membranes were probed with antibodies at a 1:500 dilution. α-tubulin was used as a loading control. Briefly described, for immunofluorescence, cells were fixed in 2% paraformaldehyde and incubated overnight with antibodies at a 1:1000 dilution. Cells were counterstained with 4′,6-diamidino-2-phenylindole (DAPI) for nuclei.

The specificity of the rabbit polyclonal antibodies for DUX4 was confirmed by Western blot and immunofluorescence. In addition, the inventors used the rabbit polyclonals to immunoprecipitate transduced lysates and then demonstrated the pull-down of DUX4 by western blot using a mouse monoclonal antibody to DUX4 (data not shown). Immunoprecipitation of lysates were performed with rabbit polyclonals bound to a 1:1 mixture of Protein A and Protein G Dynabeads (Invitrogen, CA), following manufacturer's instructions. DUX4 protein was immunoprecipitated overnight at 4° C. Precipitated material was eluted directly in Laemmli buffer and boiled for western blot. Samples were run on 4-12% gradient bis-tris polyacrylamide gel, transferred to 0.45 μm nitrocellulose membranes and probed with a custom mouse monoclonal antibody against DUX4 called P4H2. Anti-mouse kappa light chain (SouthernBiotech, Ala.) was used a secondary antibody to minimize cross reactivity against denatured rabbit IgG heavy chain.

It was further determined that the antibodies that were raised against the C-terminus of DUX4-fl do not recognize DUX4-s.

Immunoprecipitation Analysis

The inventors used two polyclonal rabbit antisera against DUX4 to immunoprecipitate DUX4-fl from human primary myoblasts 24 hours after transduction with lentiviral expressed DUX4-fl or control non-transduced primary myoblasts. Non-redundant reads unambiguously mapped to the human genome were computationally extended to a total length of 200 nucleotides and “peaks” were defined as regions where the number of reads was higher than a statistical threshold compared to the background, as described below. Reads mapping to the X and Y chromosomes were excluded from the analysis.

Chromatin Immunoprecipitation and Ultra-High-Throughput Sequencing

ChIP was performed and ChIP DNA samples were prepared as previously described in Cao et al., Dev. Cell 18:662-674 (2010), hereby incorporated herein by reference. Anti-DUX4 C-terminus rabbit polyclonal antibodies MO488 and MO489 were combined to immunoprecipitate DUX4-fl. Anti-DUX4 N-terminus polyclonal antibodies FH106 and FH107 were combined to immunoprecipitate DUX4-s. The samples were sequenced with Illumina Genome Analyzer II.

Defining Peaks

Sequences were extracted by Illumina package GApipeline and reads were aligned using BWA to the human genome (hg18). The inventors only kept one of the duplicated sequences to minimize the artifacts of PCR amplification. Each read was extended in the sequencing orientation to a total of 200 bases to infer the coverage at each genomic position. Peak calling was performed by a house developed R package “peakSig” (pending submission to Bioconductor), which model background reads by a negative binomial distribution. The negative binomial distribution can be viewed as a continuous mixture of Poisson distribution where the mixing distribution of the Poisson rate is modeled as a Gamma prior. This prior distribution is used to capture the variation of background reads density across the genome. Model parameters were estimated by fitting the truncated distribution on the number of bases with low coverage (one to three), to avoid the problem of inferring effective genome size excluding the non-mappable regions, and to eliminate contamination of any foreground signals in the high coverage regions. The inventors also fit a GC dependent mixture model so that the significance of the peaks is determined not only by peak height, but also by the GC content of the neighboring genomic regions.

Motif Analysis

Discriminative motif discovery was carried out as described in Palii et al. (2011), in which motifs were identified that distinguish a positive and a negative sequence dataset, which in this study, the positive sequences correspond to Dux4 binding sites and negative sequences correspond to the randomly sampled flanking regions of Dux4 binding sites. To generate more accurate presentation of the Dux4 binding sites from the consensus pattern returned by this analysis, the inventors tried to learn a positional weight matrix (PWM) model, using the matches of the consensus pattern as the seed to initialize the iterative expectation-maximization (EM) refinement process similar to MEME. If appropriate, the motifs are extended iteratively as long as there is sequence preference in the flanking region, and refined in the same EM process.

Electromobility Shift Assay

EMSA was performed with ³²P-labeled 31-bp oligonucleotides from endogenous genomic sequences containing the putative DUX4 binding site as probes (sequences below; only forward shown). Radiolabeled probes were incubated with in vitro translated protein generated from pCS2-DUX4-fl or pCS2-DUX4-s² vectors using the TNT SP6 Coupled Wheat Germ Extract System (Promega) according to manufacturer's instructions. To obtain supershift of protein-DNA complexes, 0.1 μg of E14-3 anti-DUX4 rabbit monoclonal antibody was added to the mixtures. For competition experiments, excess unlabeled probes of either wild-type or mutant sequences were included in the binding reaction. The gels were prepared and run as previously described (Knoepfler et al., 1999).

SEQ ID Probe Forward oligo sequence NO: TRIM48 AGGAGTGATGATAATTTAATCAGCCGTGCAA 150 TRIM48mut AGGAGTGATGATACTTTTATGAGCCGTGCAA 151 THED1 CCTGTGGGAGGTAATCCAATCATGGAGGCAG 152 THE1Dmut CCTGTGGGAGGTACTCCTATGATGGAGGCAG 153 CSF1R CCAGGTGGAGATAATTGAATCATGGGGGCAG 154 CSF1Rmut CCAGGTGGAGATACTTGTATGATGGGGGCAG 155

Association of Binding and Expression

The inventors associated a peak to its closest TSS within the region flanked by CTCF binding sites, which were identified in a ChIP-seq experiment on human CD4+ T cells (GEO accession number GSE12889/GSM325895).

Enhancer Activity Reporter Test

The DUX4 binding site in the ZSCAN4 pGL3-promoter construct was either reversed in orientation (as shown in FIG. 3D) or moved downstream of the reporter gene (as shown in FIG. 3E). Cells were co-transfected with pCS2 expression vectors (1 ug/plate) carrying either β-galactosidase or DUX4-fl and with pGL3-promoter luciferase reporter vectors (1 ug/plate). Transfections and luciferase assays were done as in main methods. Data are given as the averages±SD of triplicates.

MaLR Expression Analysis

Real-time PCR was performed as described above. Water and minus RT controls were checked to ensure there was no amplification of these repetitive elements from residual or contaminating genomic DNA. Primer sequences were:

(SEQ ID NO: 156) THE1 forward, 5′-ACCCCTCATGGAGAACCTCT-3′ and (SEQ ID NO: 157) THE1 reverse, 5′-ACCCTCTTCTCACAGCTCCA-3′.

Luciferase Assay

Transient DNA transfections of RD cells were performed using SuperFect (Qiagen) according to manufacturer specifications. Briefly, 3×10⁵ cells were seeded per 35 mm plate the day prior to transfection. Cells were co-transfected with pCS2 expression vectors (2 ug/plate) carrying either β-galactosidase, DUX4-fl or DUX4-s and with pGL3-promoter luciferase reporter vectors (1 μg/plate) carrying various putative DUX4 binding sites or mutant sites upstream of the SV40 promoter or pGL3-basic reporter vector (1 μg/plate) carrying test promoter fragment upstream of the firefly luciferase gene. Cells were lysed 24 h post-transfection in Passive Lysis Buffer (Promega). Luciferase activities were quantified using reagents from the Dual-Luciferase Reporter Assay System (Promega) following manufacturer's instructions. Light emission was measured using BioTek Synergy2 luminometer. Luciferase data are given as the averages±SD of at least triplicates.

Real-Time PCR of Targets in Matched Testis and Skeletal Muscle

Real-time PCR was performed as described above. Primer sequences for muscle markers are listed below.

Gene Forward primer Reverse primer name sequence sequence MYH2 TTCTCAGGCTTCAAGATTTGG CTGGAGCTTGCGGAATTTAG (SEQ ID NO: 158) (SEQ ID NO: 159) CKM CACCCCAAGTTCGAGGAGAT AGCGTTGGACACGTCAAATA (SEQ ID NO: 160) (SEQ ID NO: 161)

DUX4-fl PCR

Nested DUX4-fl3′ PCR on primary myoblast and muscle biopsies were performed as described herein. Primers used were:

182 forward (SEQ ID NO: 162) (5′-CACTCCCCTGCGGCCTGCTGCTGGATGA-3′) and 183 reverse (SEQ ID NO: 163) (5′-CCAGGAGATGTAACTCTAATCCAGGTTTGC-3′) nested with 1A forward (SEQ ID NO: 164) (5′-GAG CTC CTG GCG AGC CCG GAG TTT CTG-3′) and 184 reverse (SEQ ID NO: 165) (5′-GTAACTCTAATCCAGGTTTGCCTAGACAGC-3′).

Knockdown of DUX4-fl Targets

FSHD cultured myoblasts were grown to confluence and switched to differentiation media as described herein. Simultaneously, cells were transduced by lentivirus carrying DUX4-s or GFP along with 8 μg/mL polybrene. Cells were washed and changed to plain differentiation media after 24 hours. Cells were harvested for RNA after 48 hours of differentiation. Untransduced cells were used to assess baseline expression of DUX4-fl target genes.

Results:

A total of 62,028 and 39,737 peaks were identified at P-value thresholds of 10⁻¹⁰ and 10⁻¹⁵, respectively, after subtracting background peaks in the control samples. DUX4-fl peaks were widely distributed both upstream and downstream of gene transcription start sites (TSSs) with higher numbers in introns and intergenic regions, but showing a relatively constant peak density in all genomic regions when normalized for the size of the genomic compartment. This pattern differs from that reported for many other transcription factors, such as MYOD (Cao et al., 2010), that show higher average peak density in regions near TSSs.

A de novo motif analysis identified the sequence “TAAYBBAATCA” (SEQ ID NO: 166) (IUPAC nomenclature: wherein: T=Thymine; A=Adenine; Y=Pyrimidine (Cytosine (C), Thymine (T), or Uracil (U)); B=Cytosine (C), Thymine (T), Uracil (U) or Guanine (G) (not Adenine (A)); C=cytosine), near the center of greater than 90% of peaks.

To the inventor's knowledge, this motif has not been described for any other transcription factor, but does contain two canonical homeodomain binding motifs (TAAT) arranged in tandem and separated by one nucleotide. Approximately 30% of sequences under the DUX4-fl peaks also contained a second larger motif that encompasses the primary DUX4-fl binding motif. This longer motif matches the long terminal repeat (LTR) of retrotransposons.

Assessment of the representation of DUX4-fl binding at different annotated repetitive elements in the genome shows a nearly 10-fold enrichment of DUX4-fl binding in the Mammalian apparent LTR-Retrotransposon (MaLR) family of retrotransposons and some enrichment in the related ERV family, as shown in TABLE 8 below. Note that the quantitative estimate of repeat-associated binding sites is conservative since reads mapping to more than one locus are excluded from the analysis.

TABLE 8 Repeat families bound by DUX4 Overall DUX4-fl Binding Genome DUX4-fl Prevalence Prevalence Enrichment LTR/ERVL-MaLR 0.35716 0.036 9.92 LTR/ERV 0.00032 6.00E−05 5.33 LTR/ERVK 0.00803 0.0027 2.97 LTR/ERVL 0.04558 0.01823 2.50 rRNA 1.00E−04 6.00E−05 1.67 SINE/tRNA 0.00011 7.00E−05 1.57 Unknown 0.00063 0.00043 1.47 DNA/TcMar-Mariner 0.00105 0.00092 1.14 DNA/TcMar-Tigger 0.0124 0.01121 1.11 LTR/Gypsy 0.00081 0.00076 1.07 LINE/CR1 0.00356 0.00356 1.00 DNA/hAT? 0.00016 0.00017 0.94 LINE/L2 0.02978 0.03443 0.86 SINE/MIR 0.02317 0.0281 0.82 LTR/ERV1 0.01878 0.02604 0.72 Satellite 0.00068 0.00103 0.66 LINE/L1 0.0938 0.16059 0.58 DNA/hAT-Blackjack 0.00064 0.00113 0.57 Simple_repeat 0.00442 0.00836 0.53 DNA/hAT-Charlie 0.00761 0.01486 0.51 DNA/hAT-Tip100 0.00098 0.0022 0.45 Satellite/centr 0.00047 0.00243 0.19 SINE/Alu 0.00777 0.10171 0.08 DUX4-fl binding prevalence: fraction of all DUX4-fl peaks Overall genome prevalence: fraction of whole genome DUX4-fl enrichment: (DUX4-fl binding prevalence)/(overall genome prevalence)

MaLR family members expanded in the primate lineages (Smit, 1993). Thus, if DUX4-fl binding sites were carried throughout the genome during this expansion, these newer sites might have a different sequence motif compared to DUX4-fl binding sites located outside of MaLR repeats. To determine if the expansion of MaLR-associated binding sites might obscure the identification of a different DUX4 binding motif in non-repetitive elements, the inventors performed separate motif analysis of MaLR-associated sites and sites not associated with repeats; both yielded nearly identical core motifs, TAAYYBAATCA (SEQ ID NO:167) and TAAYBYAATCA (SEQ ID NO:168), respectively, but the repeat-associated motifs had slightly more flanking nucleotides preferences reflecting the LTR sequence.

Electrophoretic mobility shift assay (EMSA) confirmed that DUX4-fl binds the core motifs present in both MaLR-associated and non-repeat associated sites: TRIM48 oligos—the TAATTTAATCA (SEQ ID NO:169) core sequence found near the TRIM48 gene, CSF1R oligos—the TAATTGAATCA (SEQ ID NO:171) core sequence found within the LTR of a THE1B retroelement near the CSF1R gene, and THE1D oligos—the TAATCCAATCA (SEQ ID NO:172) core sequence found within the LTR of the THE1D retroelement. Mutation of the core nucleotides abolishes binding, including sites from both repeat and non-repeat regions: competition with cold TRIM48 oligos reduces binding whereas competition with cold TRIM48mut oligos, containing the mutated core sequence TACTTTTATGA (SEQ ID NO:170), does not; competition with the cold CSF1R and THE1D probes to their respective radioactive oligos inhibited binding, whereas competition with cold mutant CSF1Rmut and THE1Dmut oligos, containing sites TACTTCTATG (SEQ ID NO:173) and TACTCCTATGA (SEQ ID NO:174), respectively, do not. Because the DUX4-s alternative splice form retains the N-terminal DNA-binding homeodomains, the inventors hypothesized that it would bind to the same sites as DUX4-fl. EMSA confirmed that DUX4-s specifically binds the same core binding site as DUX4-fl in vitro.

Thus, these results demonstrate that DUX4-s can bind the same sequences as DUX4-fl but does not activate transcription of the same genes, which supports the prior determination that the C-terminus contains a transactivation domain (Kawamura-Saito et al., 2006).

DUX4-fl is a Transcriptional Activator

The number of DUX4-fl binding locations exceeds the number of genes that robustly increase expression in muscle cells following transduction with DUX4-fl.

A genome-wide analysis of peak height and regional gene expression shows only a weak association of binding and gene expression for DUX4-fl. To determine whether DUX4-fl binding might function as a transcriptional activator at some of the identified binding sites, DUX4 binding sites from selected genes were cloned upstream of the SV40 promoter in the pGL3-promoter luciferase construct as follows (DUX4 binding sites are underlined)

DUX4 binding site from TRIM48: (SEQ ID NO: 175) 5′ AGGAGTGATGA TAATTTAATCA GCCGTGCAA 3′ DUX4 binging site from ZSCAN4: (SEQ ID NO: 176) 5′ AATCACGTCTT TAAATCAA TCACTGACATGG 3′

The 31 bp DUX4 binding site from TRIM48 (SEQ ID NO:175) or ZSCAN4 (SEQ ID NO:176) were inserted into the luciferase reporter construct upstream of the SV40 promoter.

FIG. 2 illustrates that DUX4-fl activates transcription in vivo and DUX4-s can interfere with its activity. FIG. 2A shows reporter construct structure; Genomic fragments near the TRIM48 (FIG. 2B) and ZSCAN4 genes (FIG. 2C) containing DUX4 binding sites were cloned into pGL3-promoter reporter vector (schematic, top) and transfected into human rhabdomyoscaroma cell line RD. Cells were co-transfected with DUX4-fl or DUX4-s. pCS2-13 galactosidase (beta gal) was used to balance DNA amount in control condition. TRIM48mut and ZSCAN4mut are mutated binding sites. Luciferase activity was set relative to control.

As further shown in FIGS. 2D and 2E, DUX4-fl can act as an enhancer at certain loci. FIG. 2D shows the relative luciferase activity in the presence of DUX4-fl from a reporter construct in which the 31 bp DUX4 binding site was inserted in reverse orientation upstream of the SV40 promoter. FIG. 2E shows the relative luciferase activity from a reporter construct in which the 31 bp DUX4 binding site was inserted in the original orientation, but moved downstream of the reporter gene. The luciferase activity was set relative to control plasmid conditions and error bars represent standard deviation of triplicates.

As shown in FIG. 2, co-transfection with DUX4-fl in human rhabdomyosarcoma cell line RD significantly induced luciferase expression independent of orientation or position, and mutation of the DUX4 binding motif eliminated the induction. In contrast to DUX4-fl, DUX4-s did not activate expression despite demonstrating in vitro binding to this site.

To determine whether DUX4 binding might directly regulate transcription of select genes, the inventors cloned the 1.9 kb enhancer and promoter region of the ZSCAN4 gene that includes four DUX4 binding sites as follows: (DUX4 binding sites are underlined)

(SEQ ID NO: 177) 5′AG TAATTCAATCA ACAGACAAGTGTTATCCAATCACGTCTT TAAATC AATC A CTGACATGGAGCTGGGGCTGGATGAAGATTCCATCAG TAATTCA ATCA ACAGACAAGTGTTATCCAATCACGTCTTT AAATCAATCA CT3′

The 1.9 kb enhancer and promoter region of the ZCAN4 gene that includes the four DUX4 binding sites from ZCAN4 (SEQ ID NO:177) were inserted upstream of the luciferase reporter construct (pGL3 basic luciferase vector). Co-transfection with DUX4-fl significantly induced expression of this reporter and mutation of three of the four DUX4 binding sites nearly abolished the induction. DUX4-s interfered with the activity of DUX4-fl when the two were co-expressed, suggesting that DUX4-s acts as a dominant negative for DUX4-fl activity. DUX4-fl also activated transcription through DUX4 sites in repetitive elements: DUX4-fl activated transcription of a luciferase reporter containing DUX4 binding sites cloned from LTRs at a MaLR THE1D element and RT-PCR showed induction of endogenous MaLR transcripts in muscle cells transduced with DUX4-fl.

Discussion:

The results in this Example demonstrate that DUX4 binds to and activates transcription from endogenous retrotransposon LTRs of the MaLR family. To the inventor's knowledge, this is the first identification of a transcription factor that can regulate the expression of these repetitive elements in the human genome. The induction of DUX4 expression may be used to induce expression to create placental like invasion and tolerance in allogeneic organ transplants, or to induced mobilization of retrotransposed elements for insertional mutagenesis.

Example 3

This Example demonstrates that DUX4 targets are normally expressed in human testis but not in healthy skeletal muscle, and that DUX4 regulated genes normally expressed in the testis are aberrantly expressed in FSHD muscle.

Methods and Materials Real Time PCR

One microgram of total RNA was reverse transcribed into first strand cDNA in a 20 uL reaction using SuperScript 111 (Invitrogen) and digested with 1 U of RNase H (Invitrogen) for 20 min at 37° C. cDNA was diluted and used for quantitative PCR with iTaq SYBR Green supermix with ROX (Bio-Rad). The relative expression levels of target genes were normalized to those of ribosomal protein L13A (RPL13A) by 2^(Δct). Undetermined values were equated to zero. Standard deviations from the mean of the ΔCt values were calculated from triplicates. PCR primers used for detecting the transcripts of the selected genes are listed in Supplementary methods.

Muscle Biopsies and Human RNA

Muscle biopsy samples were collected from the vastus lateralis muscle of clinically affected and control individuals as previously described (Snider et al., 2010). RNA from matched tissues from healthy donors were purchased from BioChain (Hayward, Calif.).

Statistical Analyses

Statistical significance between two means was determined by unpaired one-tailed t tests with P-value <0.05. Statistics for the microarray and ChIP-Seq experiments are described separately.

Results: DUX4-fl Directly Regulates Genes Involved in Germline Development

To identify the set of genes that might reflect the function of DUX4-fl prior to the expansion of MaLRs in primates, the inventors identified the subset of genes activated at least 3-fold by DUX4-fl that also contain a non-repeat associated binding site within six kilobases of the TSS and not separated from the TSS by a binding site for the insulator factor CTCF, as shown in TABLE 9.

TABLE 9 Non-repeat element DUX4-fl binding sites associated with expressed genes space max.cov Full.fc Symbol dist2tss chr22 124 8.4 RFPL1 −3042 chr7 114 8.3 hCG_1651160 −892 chr7 215 8.3 hCG_1651160 −192 chr6 232 8.3 RFPL4B −321 chr19 364 8.3 ZSCAN4 1430 chr2 85 8.1 TRIM43 −5584 chr2 47 8.1 TRIM43 1385 chr11 178 7.9 TRIM48 −151 chr1 99 7.8 PRAMEF12 −1230 chr13 56 7.5 CCNA1 −2425 chr13 58 7.5 CCNA1 1874 chr22 118 7.3 RFPL2 −2853 chr22 129 7.3 RFPL2 3057 chr14 344 7 PNP −104 chr11 85 6.9 TRIM49L1 200 chr11 109 6.9 TRIM49L2 −202 chr8 55 6.4 DEFB103A −2289 chr19 110 5.5 ZNF296 182 chr11 373 4.2 SFRS2B 42 chr5 91 4.1 PPP2R2B 2498 chr20 55 4.1 ZNF217 −2168 chr20 122 4.1 ZNF217 3546 chr12 224 3.9 ZNF705A −5106 chr22 118 3.8 PANX2 −2040 chr19 98 3.8 ZSCAN5B −5014 chr19 67 3.8 ZSCAN5B −4101 chr19 89 3.8 ZSCAN5B 4892 chr16 118 3.7 SIAH1 −2337 chr12 129 3.6 FAM90A1 −1597 chr12 54 3.6 PRR4 83 chr3 117 3.4 DBR1 3981 chr11 105 3.3 SPTY2D1 −797 chr11 74 3.3 SPTY2D1 5934 chr14 117 3.2 FBXO33 −2226 chr19 83 3.2 GTF2F1 134 chr17 177 3.2 JUP −701 chr22 234 3.2 TFIP11 −1353 chr21 96 3.1 CLDN14 −2523 chr20 53 2.9 CSE1L −5914 chr20 57 2.9 CSE1L −1935 chr2 85 2.9 PELI1 4936 chr7 63 2.7 BZW2 1939 chr7 86 2.7 BZW2 1955 chr10 265 2.7 CCNJ −637 chr1 116 2.6 DENND2C −3169 chr14 257 2.6 PABPN1 −529 chr7 128 2.6 SRRT 1546 chr19 104 2.6 USP29 2090 chr19 66 2.6 USP29 3676 chr14 159 2.5 C14orf102 −558 chr11 46 2.4 CTR9 1913 chr21 229 2.4 SYNJ1 −766 chr6 159 2.3 NFYA 49 chr1 132 2.2 C1orf63 −1326 chr17 283 2.2 HOXB2 −2471 chr3 51 2.2 PVRL3 2678 chr6 250 2.1 C6orf191 61 chr10 70 2.1 CBARA1 2340 chr10 250 2.1 CBARA1 4786 chr21 244 2.1 SON −2951 chr10 56 2 AVPI1 126 chr10 200 2 FRG2B 598 chr16 46 2 RBBP6 −4040 chr16 323 2 RBBP6 −1922 chr16 76 2 RBBP6 −1619 chr1 139 1.9 EXOSC10 150 chr2 150 1.9 GPBAR1 −224 chr9 85 1.9 NANS 1843 chr20 62 1.9 SNAI1 769 chr18 65 1.9 TAF4B −1741 chr21 274 1.8 C21orf91 −803 chr2 163 1.8 CLK1 4634 chr1 93 1.8 KDM5B 301 chr12 73 1.8 KIF21A −4249 chr12 37 1.8 KIF21A −1030 chr17 43 1.8 MED13 −2755 chr10 172 1.8 SEC61A2 −1861 chr11 133 1.8 SPRYD5 −2855 chr14 50 1.7 C14orf138 −4696 chr14 53 1.7 C14orf138 326 chr12 55 1.7 DDX47 −4416 chr5 269 1.7 MAST4 −1253 chr10 57 1.7 PRPF18 3230 chr6 105 1.7 PTP4A1 −2227 chr9 198 1.6 CTNNAL1 641 chr1 205 1.6 EGLN1 −1 chr9 69 1.6 MAPKAP1 −4397 chr9 153 1.6 MAPKAP1 3619 chr2 52 1.6 RTN4 −2562 chr2 115 1.6 RTN4 1853 chr10 43 1.6 SAMD8 3338 chr9 88 1.6 SH3GL2 −4600 Chromosome: chromosome location of binding site max.cov: peak height full.fc: expression fold change for DUX4-fl targets dist2tss: distance to TSS

The 74 genes meeting these criteria are highly enriched for genes involved in stem and germ cell functions, RNA processing, and regulated components of the PolII complex, similar to the major GO categories identified for all of the genes regulated by DUX4-fl. Quantitative RT-PCR of six DUX4 regulated genes (PRAMEF1; RFPL2; TRIM43; ZSCAN4; KHDC1; MBD3L2) on paired samples of testis mRNA and skeletal muscle mRNA from two control individuals found high expression of these targets in the testes and absent, or nearly absent, expression in skeletal muscle, supporting a conserved role for DUX4 in germline biology. The inventors also detected the expression of the related DUXA and DUX1 genes in healthy testis (data not shown), further supporting the notion that this family of double homeodomain proteins has a role in germ cell biology. The results of real-time RT-qPCR analysis of gene expression in human testis versus matched skeletal muscle tissue from two healthy donors showed that DUX4 targets tested are normally expressed in human testis but not in healthy skeletal muscle. The expression results shown are presented relative to internal standard RPL13a, and error bars represent standard deviation of PCR triplicates for the following DUX-fl target genes: (A) PRAMEF1; (B) RFPL2; (C) TRIM43; (D) ZSCAN4; (E) KHDC1; (F) MBD3L2; and controls (G) MYH2 (skeletal muscle marker), (H) CKM (skeletal muscle marker), and (I) RPL13a.

DUX4-fl-Regulated Gene Targets are Expressed in FSHD Muscle

To determine whether the low levels of endogenous DUX4-fl mRNA detected in FSHD skeletal muscle is sufficient to activate DUX4 target genes, the inventors assessed the expression of some of these genes ((A) PRAMEF1; (B) RFPL2; (C) MBD3L2; (D) TRIM43; (E) KHDC1; and (F) ZSCAN4) in a set of control and FSHD muscle. Cultured muscle cells from control biopsies showed low or absent expression of the six DUX4-fl regulated genes, whereas these genes were expressed at significantly higher levels in the FSHD muscle cultures, including those from both FSHD1 and FSHD2 individuals.

The endogenous DUX4-fl expression status is provided in TABLE 10.

TABLE 10 DUX4-fl expression in FSHD and control muscle Sample # Formal Identifier DUX4-fl expression Disease Status Primary Human Myoblasts 1 MB135 not detected control 2 MB196 not detected control 3 MB201 not detected control 4 MB209 not detected control 5 MB230 not detected control 6 MB54-1* not detected control* 7 MB073 detected FSHD1 8 MB183 detected FSHD1 9 MB197 detected FSHD1 10 MB216 detected FSHD1 11 MB200 detected FSHD2 12 MB54-2* detected FSHD1* Muscle Biopsies 1 C-20 not detected control 2 C-22 not detected control 3 C-33 not detected control 4 C-38 not detected control 5 C-40 not detected control 6 C-2333/C-2397 not detected control 7 F-2315 not detected FSHD1 8 F-2316 detected FSHD1 9 F-2319 not detected FSHD1 10 F-2326 not detected FSHD1 11 F-2331 detected FSHD1 12 F-2367 detected FSHD1 13 F-2369 detected FSHD1 14 F-2377 detected FSHD1 *Myoblasts cultured from the same mosaic individual that either do not have (MB54-1) or have (MB54-2) a contracted 4q allele

The results obtained demonstrate that DUX4 regulated genes normally expressed in the testis are aberrantly expressed in FSHD muscle. Similar to the expression of DUX4-fl regulated targets in cultured FSHD muscle, muscle biopsies from FSHD individuals had readily detectable mRNA of DUX4-fl regulated genes, although at varying levels in different biopsies.

For the results of real-time RT-PCR analysis of expression of DUX4-fl target genes in Control and FSHD muscle biopsies from 15 individuals for the following target genes: (A) PRAMEF1; (B) RFPL2; (C) MBD3L2; (D) TRIM43; (E) KHDC1; and (F) ZSCAN4, it is noted that the DUX4-fl mRNA is at extremely low abundance in FSHD muscle and it is notable that some biopsy samples in which the DUX4-fl mRNA was not detected showed elevation of DUX4 regulated targets (Table 10), indicating that the target mRNA is of significantly higher abundance and perhaps more stable than the DUX4 mRNA. The DUX4 expression status in the muscle samples in Control and FSHD muscle biopsies from 15 individuals was analyzed, as determined by nested DUX4 PCR on cDNA from cultured muscle cells or biopsies. RPL13A PCR was used for an internal standard. The coded sample names and complete status information for the biopsy samples are provided in TABLE 10.

To determine whether the expression of the DUX4 target genes in FSHD muscle was due to binding of the DUX4 protein to its consensus DNA motif, the inventors used DUX4-s to interfere with DUX4-fl activity. As shown above, DUX4-s binds the same consensus motif as DUX4-fl but does not activate gene expression and co-transfection of DUX4-s with DUX4-fl interferes with the ability of DUX4-fl to activate a reporter construct.

Lentiviral expression of DUX4-s in FSHD muscle cells inhibited the endogenous expression of the target genes as well, indicating that the DUX4 target genes in FSHD muscle require an activating factor that binds at the DUX4 motif, which is most likely the DUX4-fl protein. DUX4-s blocks expression of DUX4-fl target genes in FSHD muscle cells. DUX4-s maintains the DNA binding domain of DUX4 but lacks the transcriptional activation domain and therefore acts as a dominant negative to DUX4-fl by binding to the DUX4 motif (see FIG. 2). Real-time RT-PCR quantitation of three DUX4 target genes, (A) PRAMEF1, (B) RFPL2 and (C) MBD3L2 in FSHD cultured muscle cells transduced with lenti-GFP or lenti-DUX4-s or untransduced was performed.

In summary, this data support the model that inappropriate expression of DUX4 plays a causal role in FSHD skeletal muscle pathophysiology by activating germline gene expression and endogenous retrotransposons in postmitotic skeletal muscle. Beyond their utilities as candidate biomarkers, the DUX4 targets identified in Example 1 point to specific mechanisms of disease and may help guide the development of therapies for FSHD.

Example 4

This Example demonstrates that DUX4-fl activates expression of multiple cancer testis antigens and gene families in FSHD muscle and DUX4-fl expression correlates with expression of cancer testis antigens (CTAs) in a cancer cell and CTA family members are induced by DUX4-fl in dendritic cells.

Methods and Results: DUX4-fl Activates Expression of Cancer Testis Antigens and Gene Families in FSHD Muscle

As described above in EXAMPLES 1-3, based on expression array data, many of the genes found to be activated by DUX4-fl in skeletal muscle cells are expressed in the germline, and some are close family members of cancer testis antigens. For example, DUX4-fl activates the expression of CSAG3 and PRAMEF1, as well as other PRAME family members, whereas CSAG2 and PRAME have been characterized as inducing a T-cell response to cancers.

To further analyze the expression of cancer testis antigen in the presence of DUX4-fl, an experiment was carried out in which normal skeletal muscle cells were transduced with the Lentiviral vector expressing either DUX4-fl, or a control Lentiviral vector expressing GFP, generated as described in Example 1, and the transduced cells were analyzed by RT-PCR for expression of several known cancer testis antigens. The results were normalized to an internal control standard of either 18S or GAPDH.

Seven known cancer testis antigens: BAGE, MAGEA4, MAGEA9, SSX1, SSX2, SSX4, and one of the PRAME family members are all induced over 2-fold by the expression of DUX4-fl as shown by RT-PCR analysis.

To determine whether the T-cell infiltrate associated with FSHD represents an oligoclonal response to a disease-related antigen, the T-cell receptor beta-chain was deep-sequenced from DNA isolated from a muscle biopsy from an FSHD patient. Three independent regions of the biopsy showed clonal expansion of the same small number of T-cell clones, demonstrating a clonal expansion consistent with the response to a limited set of antigens, in which a dominant clone was found to be present, representing over one million of the sequences and a small number of other clones. In contrast, deep sequencing of T-cell receptors from a control peripheral blood showed a broad representation of different T-cell receptors, the most abundant present at about 100,000 times (data not shown). Therefore, the T-cells infiltrating the FSHD skeletal muscle represent a small number of clones that have expanded, consistent with an immune response to a muscle expressed antigen.

DUX4-fl Expression Correlates with Expression of Cancer Testis Antigens (CTAs) in a Cancer Cell and CTA Family Members are Induced by DUX4-fl in Dendritic Cells

It was determined that DUX4-fl is expressed in some cancer cell lines and its expression correlates with expression of CTAs. It was further determined that the colon cancer cell line HCT116 does not express DUX4-fl but DUX4-fl expression is induced when the two major DNA methyltransferase genes are disrupted in the HCT116 double knock-out line. The results of an RT-PCR assay for DUX4-fl in HCT116 cells demonstrated that DNA methylation suppresses DUX4 expression. DUX4-fl is not detected in the parental HCT116 colon cancer cell line (wt lane), nor in the derivatives of this line that have single gene knock-outs for DNMT1 (1−/− lane) or DNMT3b (3b−/− lane); however, DUX4-fl is expressed in the double knock-out of DNMT1 and DNMT3b (DKO lane) that substantially reduces the degree of DNA CpG methylation. xxx

In addition, DUX4-fl expression can be detected in HCT116 cells treated with the demethylating agent azacytidine (decitabine). Treatment of HCT116 cells with the DNA demethylating agent 5-azacytidine (decitabine) induces the expression of DUX4-fl, as determined by RT-PCR for DUX4-fl in different tumor cell lines.

FIG. 3 is a Heat map showing expression of cancer testis antigens (CTA) in HCT116 cells under conditions that activate DUX4-fl expression (i.e., treatment with the demethylating agent 5-azacytidine). The relative expression of the CTA in each row was measured by RT-PCR and represented as high (light shading) or low (dark shading). The first column shows very low expression of CTAs in HCT116 that are not treated (−) and the second column shows a robust induction after treatment with azacytidine (+), a condition that induces expression of DUX4-fl. Similar patterns are seen with the DNMT1 and DNMT3 mutants, whereas a higher basal level of CTAs is seen in the DKO even before azacytidine treatment. Therefore, there is a strong correlation between expression of DUX4-fl and the expression of CTAs. As further shown in FIG. 3, the expression of DUX4-fl in these cells correlates with upregulation of multiple known CTAs, including BAGE, NYESO1 and MAGE and PRAME family members.

An experiment was carried out to measure the expression level of DUX4-fl regulated genes in chronic myelogenous leukemia (CML) cells using an RT-PCR assay for the target genes. The results showed that DUX4-fl regulated genes are expressed in CML cells that express the PRAME cancer testis antigen (CTA). It is noted that CML1 does not express the PRAME CTA, whereas CML2 and CML3 do express the PRAME CTA. CML2 and CML3 also express genes regulated by DUX4-fl, TRIM43 and ZSCAN4, indicating that DUX4-fl or a DUX family member is likely activating these genes in the CML cells. In CML cells, the expression of the PRAME CTA correlates with the expression of other DUX4-fl targets, indicating that DUX4-fl or another member of the DUX family, is likely the transcriptional driver of CTA expression in these cells.

Expression of DUX4-fl in HCT116 Cells Induces the Expression of the CTA Family Member PRAMEF1.

Expression of DUX4-fl in HCT116, primary dendritic cells, and in two cancer cell lines JJ and FS shows robust activation of the PRAMEF1 gene, a gene highly related to the PRAME CTA. The cancer cell lines JJ and FS are tumor cell lines derived from patients with chondrosarcomas, as described in Jagasia et al. (1996).

Results showed that expression of DUX4-fl in HCT116 cells induces the expression of the CTA family member PRAMEF1 in HCT116 wt cells. HCT116 cells were infected with a control lenti-GFP or with lenti-DUX4-fl and the abundance of PRAMEF1 mRNA measured relative to a constitutively expressed gene, RPL13a.

Results showed that expression of DUX4-fl induces expression of the CTA family member PRAMEF1 in primary dendritic cells and cancer cell lines. Primary dendritic cells and the tumor cell lines derived from patients with chondrosarcomas designated JJ and FS (described in Jagasia, et al., 1996, supra) were transduced with lentiviral constructs expressing a control gene, green fluorescent protein (GFP), or DUX4fl. PRAMEF1 mRNA was measured by real-time PCR relative to a constitutively expressed control, RPL13a.

Summary of Results:

These results demonstrate that DUX4-fl activates expression of multiple cancer testis antigens and gene families in FSHD muscle and DUX4-fl expression correlates with expression of cancer testis antigens (CTAs) in a cancer cell and CTA family members are induced by DUX4-fl in dendritic cells.

Example 5

This Example demonstrates that DUX4-fl inhibits the innate immune response induced by lenti-viral infection and further that DUX4-fl induces expression of a secreted factor that suppresses the innate immune response.

Methods and Results: DUX4-fl Inhibits the Innate Immune Response Induced by Lenti-Viral Infection.

In the experiment generating expression array data described in Example 1, the inventors surprisingly determined that lentiviral infection activates the innate immune response in human muscle cells, whereas DUX4-fl suppresses the induction of the innate immune response. In this experiment, Human myoblasts were infected with control lenti-virus expressing green fluorescent protein (lenti-GFP), DUX4-fl (lenti-DUX4-fl), or the short splice form of DUX4 that lacks the carboxyterminal region of the protein (lenti-DUX4-s). As shown previously, DUX4-s contains the DNA binding domains but lacks the carboxyterminal activation domain, and therefore binds DNA but does not activate gene transcription. RNA was harvested from the lenti-viral infected cells and uninfected control cells at 24 hours after infection.

Compared to uninfected control cells, the lenti-GFP infection induced expression of 341 genes using a 2-fold change and FDR<0.01 criteria, as shown in TABLE 11.

TABLE 11 Genes Induced by Lentiviral Constructs in Human Muscle Cells Symbol GFP/NoLenti.fc Full/GFP.fc Short/GFP.fc Full/NoLenti.fc Short/NoLenti.fc 1 IFI27 7.30 −6.53 0.27 0.92 7.60 2 MX1 7.21 −5.67 0.26 1.58 7.49 3 IFITM1 6.73 −6.12 0.34 0.73 7.08 4 IFI44L 5.75 −5.12 0.47 0.74 6.22 5 CFB 5.39 −5.62 0.63 0.07 6.04 6 HERC5 5.37 −3.20 1.33 2.21 6.71 7 SOD2 5.21 −4.62 1.53 0.67 6.75 8 IFI6 5.09 −4.24 −0.04 0.82 5.05 9 ISG15 5.06 −4.31 0.13 0.74 5.20 10 IFIT1 4.79 −4.38 0.72 0.43 5.50 11 BST2 4.69 −4.25 0.21 0.58 4.91 12 OAS1 4.38 −4.61 1.45 0.13 5.82 13 IFIT2 4.37 −4.31 2.07 0.20 6.44 14 EPSTI1 4.36 −4.12 0.66 0.34 5.05 15 LOC100129681 4.24 −4.07 0.52 0.34 4.75 16 SERPINA3 4.12 −2.22 −0.29 1.89 3.83 17 STAT1 3.95 −2.92 0.82 1.08 4.79 18 HERC6 3.89 −3.73 0.52 0.32 4.41 19 MX2 3.85 −4.07 0.96 0.07 4.80 20 SAA1 3.85 −4.14 0.26 0.03 4.11 21 TNFAIP6 3.80 −2.21 1.31 1.63 5.10 22 CCL20 3.73 0.11 1.63 3.84 5.35 23 OAS3 3.73 −4.03 0.87 −0.09 4.59 24 IFIH1 3.69 −3.70 1.66 0.25 5.34 25 LY6E 3.69 −3.25 0.25 0.44 3.94 26 IFIT3 3.68 −3.86 1.81 0.04 5.49 27 ECGF1 3.59 −4.30 0.62 −0.66 4.21 28 IL8 3.52 −3.88 1.19 −0.13 4.69 29 C1QTNF1 3.51 −3.85 0.77 −0.12 4.28 30 HLA-B 3.45 −2.75 0.34 0.70 3.78 31 C1R 3.43 −2.83 0.49 0.67 3.92 32 IFI35 3.41 −3.85 0.92 −0.32 4.33 33 IFI44 3.29 −2.42 0.29 0.90 3.59 34 CXCL1 3.16 −3.52 0.20 −0.04 3.36 35 SLC15A3 3.13 −3.75 0.78 −0.51 3.91 36 PRIC285 3.01 −2.61 0.86 0.45 3.87 37 SAMD9 2.93 −2.86 1.40 0.13 4.32 38 CHI3L2 2.88 −2.70 0.26 0.43 3.14 39 FOS 2.87 1.08 0.47 3.94 3.33 40 IRF7 2.86 −1.96 1.14 1.02 3.99 41 PARP12 2.85 −3.17 0.78 −0.17 3.62 42 VWCE 2.84 −3.32 −0.12 −0.22 2.72 43 EIF2AK2 2.72 −2.30 0.54 0.45 3.27 44 MT1M 2.70 −2.92 1.19 −0.17 3.90 45 LGALS3BP 2.68 −2.12 0.31 0.57 3.00 46 VCAM1 2.68 −3.01 0.63 −0.11 3.31 47 XAF1 2.66 −3.62 0.62 −0.83 3.27 48 AGRN 2.63 −2.61 0.38 0.10 3.01 49 TMEM140 2.61 −2.95 1.00 −0.03 3.59 50 PARP14 2.58 −2.83 0.52 −0.09 3.10 51 FBXO32 2.57 −1.18 0.77 1.41 3.33 52 S1PR3 2.56 −2.12 1.13 0.53 3.68 53 TAP1 2.55 −3.26 0.70 −0.70 3.26 54 SP110 2.52 −2.94 1.15 −0.33 3.66 55 NAMPT 2.51 −0.58 1.21 1.95 3.72 56 HLA-E 2.49 −1.11 0.81 1.37 3.30 57 CCL5 2.47 −2.53 1.89 0.22 4.33 58 HIST2H2AA3 2.46 1.29 1.07 3.74 3.52 59 PSMB9 2.43 −3.14 0.95 −0.53 3.37 60 IRF9 2.43 −2.25 0.29 0.20 2.72 61 CCL2 2.39 −2.68 0.44 0.01 2.82 62 OAS2 2.38 −2.71 0.46 0.00 2.82 63 SAMD9L 2.37 −2.53 1.26 −0.04 3.62 64 CD68 2.37 −1.09 1.18 1.28 3.54 65 DHX58 2.35 −2.84 0.70 −0.17 3.04 66 USP18 2.32 −2.50 1.00 0.09 3.29 67 ISG20 2.30 −2.94 2.36 −0.38 4.63 68 KIAA0247 2.30 −2.13 0.37 0.29 2.66 69 ABCA1 2.29 −1.21 −0.32 1.10 1.97 70 UBE2L6 2.26 −3.08 0.58 −0.83 2.84 71 PTX3 2.26 −2.74 0.94 −0.18 3.19 72 SLC7A2 2.26 −2.48 −0.11 −0.13 2.15 73 RARRES3 2.25 −2.22 1.27 0.20 3.51 74 HIST2H2AA4 2.24 1.31 1.07 3.54 3.30 75 TRIM22 2.24 −2.58 −0.02 −0.26 2.22 76 DDR2 2.23 −2.22 0.63 0.05 2.86 77 TNFAIP3 2.22 −2.90 0.28 −0.38 2.50 78 IGFBP4 2.22 −1.94 0.40 0.30 2.64 79 GBP2 2.19 −2.40 0.66 −0.19 2.87 80 C10orf10 2.19 −2.64 0.14 −0.32 2.33 81 NFKBIA 2.19 −3.00 0.28 −0.83 2.46 82 TRIM25 2.18 −2.51 0.51 −0.27 2.69 83 STOM 2.17 −2.29 0.62 −0.10 2.80 84 PARP9 2.13 −2.10 0.44 0.15 2.56 85 DDX58 2.12 −2.47 0.02 −0.18 2.14 86 SP100 2.10 −2.28 1.22 0.08 3.29 87 DKK1 2.06 −2.29 0.47 −0.24 2.53 88 MIR1978 2.06 −1.28 0.09 0.79 2.14 89 RSAD2 2.05 −2.40 2.36 −0.06 4.38 90 HLA-C 2.04 −1.79 0.60 0.32 2.65 91 CEBPD 2.03 −1.52 0.16 0.49 2.19 92 IL18BP 2.01 −1.25 1.40 0.85 3.37 93 2.00 −2.51 −0.13 −0.25 1.88 94 SUSD2 2.00 −1.40 −2.02 0.69 0.15 95 IFITM3 1.98 −1.95 −0.13 −0.01 1.84 96 MT1X 1.98 −2.44 0.32 −0.47 2.29 97 SHISA5 1.98 −1.76 −0.27 0.22 1.69 98 MSI2 1.97 −1.76 1.33 0.28 3.29 99 ZBTB16 1.97 −2.04 0.49 0.11 2.45 100 XPC 1.95 −2.46 0.26 −0.48 2.21 101 SPATA18 1.94 −1.99 −0.21 0.08 1.73 102 TRIM21 1.94 −1.36 0.98 0.63 2.91 103 SESN1 1.94 −1.58 −0.11 0.40 1.83 104 UGCG 1.93 −0.89 1.45 1.04 3.37 105 STAT2 1.92 −2.69 0.19 −0.77 2.11 106 RTP4 1.88 −2.28 1.21 −0.09 3.05 107 FST 1.88 −1.81 0.91 0.08 2.79 108 HLA-F 1.87 −1.93 0.94 0.14 2.79 109 DDX60 1.86 −2.35 0.45 −0.26 2.30 110 NFKBIZ 1.85 −1.57 −0.26 0.30 1.58 111 NFIL3 1.84 −1.82 0.32 0.07 2.16 112 IFI16 1.84 −2.01 0.68 −0.14 2.52 113 APCDD1 1.82 −1.89 −0.43 0.11 1.41 114 CXCL5 1.80 −2.47 0.82 −0.37 2.60 115 DCN 1.78 −1.67 0.26 0.22 2.04 116 TAPBP 1.78 −1.84 0.47 −0.04 2.25 117 CMBL 1.78 −1.99 0.07 −0.18 1.85 118 PAPPA 1.77 −2.26 0.40 −0.26 2.16 119 GRINA 1.77 −1.43 0.47 0.37 2.24 120 GDF15 1.77 −2.17 0.92 −0.28 2.69 121 LNPEP 1.76 −1.35 2.08 0.48 3.82 122 ZNFX1 1.75 −2.13 0.82 −0.35 2.56 123 LAP3 1.75 −1.55 1.40 0.21 3.16 124 PSMB8 1.74 −2.25 0.71 −0.39 2.45 125 MAMDC2 1.73 −1.86 −0.03 −0.11 1.71 126 GFPT2 1.73 −1.61 0.05 0.14 1.78 127 UBA7 1.72 −2.56 0.57 −0.69 2.29 128 SLC2A5 1.72 −1.96 0.81 −0.10 2.52 129 SLC44A1 1.71 −1.13 0.78 0.61 2.49 130 C19orf66 1.71 −2.35 0.62 −0.46 2.32 131 SERPING1 1.69 −1.67 1.21 0.23 2.87 132 STXBP6 1.69 −2.23 −0.14 −0.52 1.54 133 HIST1H2AC 1.68 0.26 1.07 1.92 2.70 134 TSC22D3 1.68 −1.73 0.20 0.03 1.87 135 PARP10 1.67 −2.06 0.54 −0.13 2.19 136 COL7A1 1.67 −2.12 −0.19 −0.41 1.49 137 ZC3H12A 1.66 −1.55 0.54 0.29 2.18 138 HIPK3 1.66 −0.30 1.55 1.39 3.15 139 GBP1 1.66 −2.24 1.01 −0.54 2.66 140 LOC729009 1.66 −2.65 0.66 −1.00 2.32 141 TNFSF13B 1.65 −1.76 2.19 0.12 3.78 142 TGFBR3 1.64 −1.34 0.46 0.43 2.08 143 CABC1 1.64 −1.49 −0.18 0.22 1.47 144 PLEKHA4 1.64 −1.46 1.33 0.24 2.95 145 NDRG1 1.63 −2.33 0.66 −0.66 2.29 146 GALNTL2 1.63 −1.83 0.99 0.03 2.58 147 PDK4 1.62 −1.52 0.03 0.29 1.64 148 ERAP2 1.62 −1.61 0.77 0.05 2.38 149 CXCL6 1.61 −1.99 0.17 −0.10 1.77 150 LOC387763 1.60 −1.46 0.20 0.32 1.80 151 CYP27A1 1.60 −1.60 −0.06 0.04 1.54 152 FTHL3 1.58 −2.58 0.45 −0.97 2.04 153 PHF11 1.57 −2.27 0.66 −0.66 2.22 154 CYBASC3 1.57 −1.95 −0.42 −0.35 1.15 155 MLKL 1.57 −2.99 1.46 −1.15 3.01 156 CYP26B1 1.56 −1.46 0.41 0.20 1.96 157 ZNF650 1.55 −1.02 0.69 0.59 2.23 158 FUCA1 1.55 −1.61 0.29 0.02 1.84 159 C9orf169 1.55 −2.51 −0.05 −0.79 1.50 160 RORA 1.55 0.89 1.89 2.40 3.38 161 DUSP19 1.52 −2.38 0.75 −0.84 2.28 162 EVC 1.51 −1.95 −0.39 −0.37 1.14 163 IL7R 1.51 −2.26 0.57 −0.49 2.05 164 CA12 1.51 −2.63 0.95 −0.85 2.44 165 FOXQ1 1.49 −1.43 0.64 0.27 2.07 166 PSME1 1.49 −1.14 0.28 0.33 1.76 167 PCTK3 1.48 −1.64 0.59 0.07 2.03 168 HIST2H2AC 1.47 1.31 0.96 2.77 2.42 169 CFD 1.46 −1.20 0.25 0.37 1.70 170 C4orf34 1.46 −1.04 0.61 0.42 2.06 171 SGK 1.45 2.04 −0.11 3.50 1.34 172 PDPN 1.45 −1.62 −0.29 −0.09 1.17 173 C18orf56 1.45 −1.62 0.21 −0.06 1.66 174 PTGFR 1.45 −1.09 0.15 0.45 1.59 175 SERPINE2 1.44 −1.37 0.20 0.07 1.65 176 AHR 1.44 1.50 1.64 2.90 3.04 177 MUC1 1.43 −1.74 0.35 −0.14 1.77 178 RN7SK 1.43 1.06 0.47 2.42 1.86 179 LOC643384 1.42 −2.22 1.02 −0.76 2.43 180 RTN1 1.42 −1.35 −0.06 0.23 1.37 181 MAOA 1.42 −1.71 −0.38 −0.08 1.07 182 MYBPHL 1.41 −1.49 −0.52 0.02 0.91 183 SPPL2A 1.41 −0.75 1.12 0.66 2.52 184 ANPEP 1.40 −2.12 0.36 −0.69 1.76 185 LOC389386 1.40 −1.52 1.37 −0.06 2.76 186 BTN3A2 1.40 −1.76 0.34 −0.18 1.72 187 CENTG2 1.39 −1.31 0.52 0.12 1.91 188 NT5C3 1.39 −0.66 1.88 0.73 3.26 189 CA9 1.38 −1.53 0.52 0.07 1.87 190 KRT17 1.38 −1.63 0.46 −0.03 1.81 191 OSBPL8 1.37 1.95 1.05 3.27 2.39 192 C4orf18 1.37 −1.78 −0.51 −0.38 0.86 193 TP53INP1 1.37 −1.14 −0.57 0.26 0.81 194 ADAR 1.36 −2.34 0.31 −0.96 1.68 195 APOBEC3G 1.36 −2.01 1.41 −0.39 2.72 196 IRAK3 1.35 −1.50 1.05 0.01 2.37 197 CST3 1.35 −1.13 0.16 0.24 1.53 198 C13orf15 1.35 1.35 −0.26 2.63 1.12 199 RRM2B 1.35 −1.01 0.62 0.42 1.95 200 CCND2 1.35 −1.06 −0.53 0.30 0.82 201 BTN3A3 1.34 −1.62 0.40 −0.05 1.72 202 EEA1 1.34 −0.96 1.03 0.50 2.31 203 RIOK3 1.34 −0.52 1.13 0.81 2.46 204 GBP4 1.34 −1.48 2.34 0.08 3.58 205 PSME2 1.33 −1.48 0.43 −0.13 1.78 206 MTSS1 1.33 −1.16 −0.41 0.26 0.94 207 RELB 1.33 −1.39 0.29 0.13 1.59 208 MUSK 1.32 −1.35 0.62 0.14 1.91 209 IL1R1 1.32 −1.34 0.30 0.09 1.61 210 CEBPB 1.32 −2.44 0.28 −1.13 1.59 211 TNFRSF6B 1.31 −1.68 0.01 −0.29 1.32 212 CSF3 1.31 −1.63 0.81 −0.07 2.06 213 ARID4B 1.30 1.40 0.57 2.69 1.86 214 HLA-H 1.30 −1.80 0.33 −0.37 1.62 215 CIDEC 1.30 −1.31 −0.03 0.17 1.27 216 MT1G 1.29 −1.27 0.25 0.05 1.55 217 FTHL11 1.29 −2.09 0.60 −0.77 1.89 218 IFITM2 1.29 −1.71 0.01 −0.46 1.29 219 RBM43 1.29 −1.52 0.32 −0.07 1.59 220 ABI3BP 1.29 −1.27 −0.41 0.04 0.89 221 MMP7 1.28 −1.27 0.21 0.22 1.48 222 C6orf138 1.28 −1.31 0.98 0.11 2.23 223 NFE2L2 1.28 −1.09 0.33 0.20 1.61 224 HIPK2 1.27 −1.17 0.36 0.12 1.63 225 FRMD3 1.26 −1.12 −0.29 0.26 1.00 226 ARFGEF2 1.26 0.13 1.34 1.38 2.54 227 C14orf159 1.26 −2.07 0.52 −0.70 1.77 228 OASL 1.25 −1.33 1.74 0.13 2.88 229 GAS1 1.25 −1.73 0.01 −0.48 1.26 230 HCG4 1.25 −1.65 0.68 −0.38 1.92 231 YPEL3 1.25 −1.28 −0.27 0.01 0.98 232 SLC39A8 1.24 −1.22 0.90 0.15 2.11 233 CYGB 1.24 −1.40 0.16 0.02 1.39 234 BTG2 1.24 −1.57 −0.12 −0.28 1.12 235 CLDN15 1.24 −1.55 −0.37 −0.07 0.91 236 BCL6 1.24 −1.26 0.36 −0.01 1.60 237 MMP3 1.24 −1.51 0.28 −0.05 1.50 238 EGFR 1.24 −1.39 1.21 −0.06 2.42 239 UNC93B1 1.23 −1.96 0.94 −0.64 2.17 240 MT1F 1.22 −1.18 −0.54 0.08 0.70 241 HLA-A 1.22 −1.08 0.56 0.15 1.80 242 TP53I3 1.22 −1.96 0.19 −0.72 1.41 243 HECW2 1.22 −1.17 0.06 0.17 1.27 244 LOC653879 1.22 −1.42 0.33 0.02 1.51 245 IGFBP5 1.22 −1.44 0.18 −0.07 1.38 246 SLC22A18 1.21 −1.56 −0.05 −0.23 1.16 247 FILIP1L 1.21 −1.78 0.07 −0.51 1.28 248 TNFRSF14 1.21 −2.72 0.57 −1.36 1.78 249 CES2 1.21 −2.04 0.06 −0.80 1.27 250 H1F0 1.21 −2.43 0.50 −1.15 1.71 251 C1RL 1.21 −1.63 −0.16 −0.24 1.06 252 PPAP2A 1.21 −1.11 0.54 0.13 1.75 253 RNU6-15 1.21 1.01 0.71 2.22 1.91 254 HIST2H2BE 1.21 1.35 0.27 2.51 1.46 255 SSH2 1.20 −1.28 −0.32 −0.05 0.89 256 DNAJC3 1.19 0.87 1.60 2.02 2.74 257 MR1 1.19 −1.28 0.68 0.01 1.85 258 SPTLC3 1.19 −1.44 0.24 −0.11 1.42 259 TCEA3 1.19 −1.71 −0.12 −0.50 1.07 260 JUNB 1.19 −1.06 0.52 0.23 1.67 261 NACC2 1.18 −1.79 0.98 −0.43 2.14 262 PHLDA3 1.18 −1.56 0.20 −0.34 1.38 263 TTC39B 1.18 −1.26 1.23 0.03 2.37 264 SCHIP1 1.18 −2.09 0.06 −0.81 1.24 265 CFLAR 1.17 −1.94 0.53 −0.70 1.71 266 ATL3 1.17 −1.46 1.35 −0.26 2.51 267 ACSM5 1.17 −1.34 0.05 −0.04 1.22 268 DRAM1 1.17 −1.09 −0.36 0.11 0.81 269 LTBR 1.17 −1.15 0.41 0.02 1.57 270 SUSD1 1.17 −1.30 0.51 −0.05 1.67 271 FTH1 1.17 −2.03 −0.42 −0.84 0.76 272 SLC7A11 1.17 −1.36 1.35 0.03 2.43 273 DDX60L 1.17 −1.64 0.66 −0.29 1.80 274 CORO6 1.15 −1.12 −0.30 0.06 0.86 275 UGP2 1.15 −1.17 0.11 0.02 1.26 276 LUM 1.15 −1.13 0.39 0.04 1.54 277 NDUFA4L2 1.15 −1.27 0.19 0.03 1.33 278 PTGES 1.15 −1.63 0.31 −0.26 1.44 279 DGKA 1.15 −1.96 0.10 −0.59 1.24 280 C1S 1.14 −1.19 0.42 0.16 1.52 281 TAP2 1.14 −1.25 1.35 0.04 2.44 282 CABYR 1.13 −1.76 −0.04 −0.46 1.09 283 MOCOS 1.13 −1.72 0.42 −0.53 1.55 284 ALDH3A2 1.13 −1.28 −0.20 −0.12 0.93 285 FTHL8 1.12 −2.35 0.51 −1.23 1.64 286 KYNU 1.12 −1.31 1.46 0.03 2.46 287 NRCAM 1.11 −1.30 −0.11 0.00 1.01 288 PYGB 1.11 −2.05 −0.12 −0.91 0.99 289 ZFHX3 1.11 −1.76 0.50 −0.59 1.61 290 ITPRIP 1.10 −1.76 0.55 −0.61 1.66 291 ASAM 1.10 −1.26 0.02 −0.04 1.12 292 MTE 1.10 −2.38 0.50 −1.25 1.60 293 SLC39A14 1.10 −1.87 0.48 −0.65 1.57 294 STK17B 1.09 −0.06 1.31 1.03 2.39 295 PSTPIP2 1.09 −1.38 0.48 −0.09 1.53 296 CXCL2 1.09 −1.34 0.00 −0.04 1.09 297 MME 1.09 −1.05 −0.18 0.05 0.90 298 SEMA4B 1.09 −1.94 0.15 −0.66 1.23 299 COPS8 1.08 −1.26 0.14 −0.15 1.23 300 HLA-G 1.08 −1.36 0.12 −0.12 1.19 301 TDRD7 1.08 −1.06 1.07 0.11 2.12 302 SLC30A1 1.08 −0.35 1.24 0.76 2.27 303 BCL3 1.08 −1.23 −0.04 −0.12 1.03 304 SRGN 1.08 −1.87 0.20 −0.80 1.28 305 LOC100133866 1.07 −1.34 −0.13 −0.18 0.95 306 TNFSF10 1.07 −1.13 2.97 0.14 3.88 307 AK3 1.07 −1.26 −0.43 −0.18 0.65 308 IFIT5 1.07 −1.65 −0.28 −0.36 0.81 309 NCOA7 1.07 1.31 −0.06 2.36 1.01 310 PDE4B 1.07 −1.14 0.68 0.11 1.68 311 DDB2 1.07 −1.41 0.11 −0.16 1.16 312 FKBP5 1.06 −1.76 −0.10 −0.71 0.95 313 LEPR 1.06 −1.00 −0.55 0.10 0.53 314 APOOL 1.06 −0.58 1.37 0.53 2.39 315 BATF2 1.05 −1.28 1.38 −0.02 2.32 316 FLT3LG 1.05 −1.07 0.39 0.13 1.40 317 FBXO6 1.05 0.03 1.02 1.08 1.99 318 IDS 1.04 −1.02 0.67 0.05 1.69 319 SLU7 1.04 1.51 0.72 2.53 1.74 320 HIST1H4H 1.04 1.03 1.23 1.97 2.16 321 PCBP3 1.04 −1.12 0.21 0.02 1.24 322 SAA2 1.04 −1.22 0.28 0.02 1.29 323 ANKRA2 1.04 −1.26 0.34 −0.14 1.36 324 C3 1.03 −1.00 0.25 0.21 1.25 325 STC1 1.03 −1.57 0.81 −0.43 1.82 326 TNFRSF10A 1.03 −1.13 0.84 0.07 1.81 327 KIAA1618 1.03 −1.84 −0.30 −0.72 0.74 328 KLF9 1.02 −1.26 −0.05 −0.22 0.97 329 PLXNB1 1.02 −1.44 −0.10 −0.34 0.93 330 CASP1 1.02 −1.17 2.17 0.05 3.02 331 PLA2G4C 1.01 −1.43 0.07 −0.29 1.09 332 LOC644423 1.01 −1.35 0.00 −0.23 1.02 333 TRIM55 1.01 −1.05 0.20 −0.04 1.22 334 TNFAIP2 1.01 −1.59 0.06 −0.42 1.06 335 SSBP2 1.01 −1.29 0.35 −0.26 1.36 336 RND3 1.01 1.39 0.93 2.37 1.92 337 TLR3 1.00 −1.27 1.67 −0.06 2.56 338 UBR1 1.00 −0.09 1.11 0.92 2.03 339 C1orf57 1.00 −1.12 0.35 −0.09 1.36 340 HOXC13 1.00 −1.11 0.44 −0.09 1.45 341 PTGER2 1.00 −1.18 −0.20 −0.18 0.80

As shown in TABLE 11, of these 341 genes induced by lenti-GFP infection, 315 were induced 2-fold or more by the lenti-DUX4-s infection. The majority of these genes are known to be in the innate immune response pathway and are likely to be induced by the introduction of the lenti-viral RNA. However, of the 341 genes induced by lenti-GFP, only 34 were induced two-fold or more by DUX4-fl and only 24 were induced within 50% of the level of induction by the lenti-GFP. Therefore, these results show that the expression of DUX4-fl suppresses the induction of 317 out of 341 (93%) lentivirus-induced genes.

Further in this regard, it is noted that DUX4-fl suppresses the induction of the three primary sensors of viral RNA (LGP2 (DHX58), IFIH1 (MDA5), and DDX58 (RIG-1)), which both positively activate their own transcription and also activate the transcription of additional transcription factors, such as IRF1 and IRF7, as shown in FIG. 2 of Sandling et al., (2011), hereby incorporated herein by reference. With continued reference to FIG. 2 of Sandling, et al., it is further noted that DUX4-fl suppressed the induction of these additional specific genes was observed (TNFAIP3, TBK1, NFKB activation, IKBKE, IRF1, IRF7, TLR3, STAT2, STAT1, IRF9, IL8, CXCL10, TNFSF138). It was further noted that DUX4-fl suppressed the induction of the following close homologues to the genes shown in FIG. 2 of Sandling, et al. (TRAM, TRIF, IFNAR2, TNFSF4).

As shown below in TABLE 12, both IRF1 and IRF7 induction is suppressed by DUX4-fl, as well as multiple components of the downstream pathway, including NFKB, interferons, STATS, TNF family members and cytokines.

TABLE 12 Representative Genes Induced by Lenti-GFP and Lenti-DUX4-s but poorly induced by Lenti-DUX4-fl (log2 fold change: GFP = control-lenti; Full = DUX4-fl, Short = DUX4-s; NoLenti = uninfected) Genbank Ref Symbol No.* GFP/NoLenti.fc Full/GFP.fc Short/GFP.fc Full/NoLenti.fc Short/NoLenti.fc Immediate Responders IFIH1 NM_022168.2 3.69 −3.70 1.66 0.25 5.34 (MDA5) DDX58 NM_014314.3 2.12 −2.47 0.02 −0.18 2.14 DHX58 NM_024119.2 2.35 −2.84 0.70 −0.17 3.04 (LGP2) Representative genes in the Pathway TNFAIP3 NM_006290.2 2.22 −2.90 0.28 −0.38 2.50 TNFAIP6 NM_007115.2 3.80 −2.21 1.31 1.63 5.10 TNFSF13B NM_006573.3 1.65 −1.76 2.19 0.12 3.78 TNFRSF6B NM_032945.2 1.31 −1.68 0.01 −0.29 1.32 TNFRSF14 NM_003820.2 1.21 −2.72 0.57 −1.36 1.78 TNFSF10 NM_003810.2 1.07 −1.13 2.97 0.14 3.88 TNFRSF10A NM_003844.2 1.03 −1.13 0.84 0.07 1.81 TNFAIP2 NM_006291.2 1.01 −1.59 0.06 −0.42 1.06 IRF7 NM_004029.2 2.86 −1.96 1.14 1.02 3.99 IRF9 NM_006084.4 2.43 −2.25 0.29 0.20 2.72 NFKBIA NM_020529.1 2.19 −3.00 0.28 −0.83 2.46 NFKBIZ NM_001005474.1 1.85 −1.57 −0.26 0.30 1.58 IL7R NM_002185.2 1.51 −2.26 0.57 −0.49 2.05 IL8 NM_000584.2 3.52 −3.88 1.19 −0.13 4.69 IL18BP NM_173042.2 2.01 −1.25 1.40 0.85 3.37 NFIL3 NM_005384.2 1.84 −1.82 0.32 0.07 2.16 IL1R1 NM_000877.2 1.32 −1.34 0.30 0.09 1.61 CXCL1 NM_001511.1 3.16 −3.52 0.20 −0.04 3.36 CXCL5 NM_002994.3 1.80 −2.47 0.82 −0.37 2.60 CXCL6 NM_002993.2 1.61 −1.99 0.17 −0.10 1.77 CXCL2 NM_002089.3 1.09 −1.34 0.00 −0.04 1.09 STAT1 NM_007315.2 3.95 −2.92 0.82 1.08 4.79 STAT2 NM_005419.2 1.92 −2.69 0.19 −0.77 2.11 TLR3 NM_003265.2 1.00 −1.27 1.67 −0.06 2.56 IFI27 NM_005532.3 7.30 −6.53 0.27 0.92 7.60 IFITM1 NM_003641.3 6.73 −6.12 0.34 0.73 7.08 IFI44L NM_006820.1 5.75 −5.12 0.47 0.74 6.22 MX1 NM_002462.2 7.21 −5.67 0.26 1.58 7.49 IFITM1 NM_003641.3 6.73 −6.12 0.34 0.73 7.08 IFI44L NM_006820.1 5.75 −5.12 0.47 0.74 6.22 IFI6 NM_022872.2 5.09 −4.24 −0.04 0.82 5.05 IFIT1 NM_001548.3 4.79 −4.38 0.72 0.43 5.50 IFIT3 NM_001549.2 3.68 −3.86 1.81 0.04 5.49 IFI35 NM_005533.2 3.41 −3.85 0.92 −0.32 4.33 IFI44 NM_006417.3 3.29 −2.42 0.29 0.90 3.59 CCL5 NM_002985.2 2.47 −2.53 1.89 0.22 4.33 CCL2 NM_002982.3 2.39 −2.68 0.44 0.01 2.82 IFITM3 NM_021034.2 1.98 −1.95 −0.13 −0.01 1.84 IFI16 NM_005531.1 1.84 −2.01 0.68 −0.14 2.52 IFITM2 NM_006435.2 1.29 −1.71 0.01 −0.46 1.29 IFIT5 NM_012420.1 1.07 −1.65 −0.28 −0.36 0.81 GFP/NoLenti, Expression ratio of lenti-GFP infected vs not infected; Full/GFP.fc, expression ratio of lenti-DUX4-fl to lenti-GFP Short/GFP.fc, Expression ratio of lenti-DUX4-s to lenti-GFP; Full/NoLenti.fc, expression ratio of lenti-DUX4-fl to no infection; Short/NoLenti.fc, Expression ratio of lenti-DUX4-s to no infection. *The sequence of each Genbank No. referenced in TABLE 12 is hereby incorporated by reference herein, with reference to Genbank accessed on Jul. 27, 2011.

Because GFP and DUX4-s do not have any significant sequence similarities on the RNA or protein level, the inventors concluded that the common set of genes activated by lenti-GFP and lenti-DUX4-s represent a response to the viral RNA that activates a common innate immune response pathway. Because DUX4-fl differs from DUX4-s primarily by lacking a transcriptional activation domain, the inventors further concluded that transcriptional activation of a gene or genes by DUX4-fl suppresses the innate immune response.

DUX4-fl Induces Expression of a Secreted Factor that Suppresses the Innate Immune Response

It was determined that DEFB103A (SEQ ID NO:49) and DEFB103B (SEQ ID NO:107), each encoding the polypeptide DEFB103A/B set forth as SEQ ID NO:178, are both activated by lenti-DUX4-fl and not by lenti-DUX4-s or lenti-GFP. These represent transcripts from a duplicated beta-defensin 3 gene, which can function as a suppressor of inflammation. As a secreted protein, DEFB103A/B (SEQ ID NO:178) has the potential to suppress the innate immune response in cells infected with lenti-GFP. As an initial step toward testing this, the inventors transduced cells with lenti-DUX4-fl or nothing for 12 hrs, washed extensively and replaced the culture media, then after an additional 12 hrs transferred the conditioned media to cells infected 24 hrs earlier with lenti-GFP.

Results of a RT-PCR assay showed that conditioned media from lenti-DUX4-fl transduced cells suppresses the induction of IFIH1 by lenti-GFP transduced cells. Cultured human muscle cells (54-1) were transduced with nothing (first lane panels A and B), lenti-DUX4-fl @ approximately MOI=10 (lane 2), lenti-DUX4-fl MOI ˜1 (lane 3), lenti-GFP MOI ˜10 (lane 4), lenti-GFP transduced cells exposed to conditioned media from lane 2 cells (lane 5), lenti-GFP transduced cells exposed to conditioned media from lane 3 cells (lane 6), lenti-GFP transduced cells exposed to media from lane 5 cells that was filtered through a 35 kD cut-off filter. The conditioned media from the lenti-DUX4 transduced cells suppresses the IFIH1 induction by lenti-GFP (Panel A). Filtering through a 35 kD filter does not remove all of the factor(s) responsible for the suppression. Lenti-DUX4-fl induces expression of DEFB103A/B, whereas the conditioned media does not, nor does lenti-GFP.

Thus, in cells infected without exposure to DUX4-fl conditioned medium, qRT-PCR confirmed that lenti-GFP activated IFIH1 and lenti-DUS4-fl did not; whereas lenti-GFP did not activate DEFB103A/B and DUX4-fl did. Conditioned media from lenti-DUX4 transduced cells suppressed the activation of IFIH1 by lenti-GFP, but did not induce expression of defensin B. Therefore, the inventors concluded that at least part of the suppression of the innate immune response by DUX4-fl is through a secreted factor, which might be DEFB103A/B.

Summary of Results

The results described in this example demonstrates that DUX4-fl inhibits the innate immune response induced by lenti-viral infection and further that DUX4-fl induces expression of a secreted factor that suppresses the innate immune response.

Example 6

This Example demonstrates that an agent known to inhibit the histone demethylase LSD1 suppresses DUX4 mRNA levels, and an agent that modifies translation dependent nonsense mediated decay stabilizes DUX4 mRNA levels.

Methods and Results:

An Agent Previously Shown to Inhibit the Histone Demethylase LSD1 can Suppress DUX4 mRNA Levels

The inventors' previous work demonstrated that DUX4 expression is epigenetically repressed and the inefficient repression of DUX4 that causes FSHD is correlated with decreased repressive histone methylation at lysine nine of histone 3 (H3K9 methylation). The monamine oxidase inhibitor pargyline has been reported to inhibit the activity of the LSD1 histone demethylase that demethylates H3K9. Treatment of FSHD muscle cultures with pargyline suppresses the expression of DUX4 mRNA expression, whereas an MAO inhibitor with a different spectrum of activity does not alter DUX4 mRNA levels.

Results showed that pargyline decreases the amount of DUX4 mRNA in FSHD muscle cells (FIG. 4). FSHD muscle cells that express endogenous DUX4-fl mRNA were treated with the MAO inhibitor pargyline that has been reported to inhibit the histone demethylase LSD1, or with another MAO inhibitor tranylcypromine that has a different spectrum of activity. The pargyline decreases the abundance of DUX4-fl mRNA in a dose-dependent manner as measured by quantitative RT-PCR while tranylcypromine had no inhibitory effect as compared to control.

Results showed that pargyline has a dose-dependent inhibition of DUX4 mRNA expression in FSHD muscle cells (FIG. 5). Cultured FSHD muscle cells were differentiated for 48 hours in differentiation medium (DM) with varying amounts of pargyline and the amount of DUX4-fl mRNA was measured by RT-PCR. There was a dose-dependent inhibition of DUX4 expression (top panel). Middle panel is a no RT control and bottom panel is a GAPDH loading control.

The inventors conclude that agents that increase chromatin mediated repression, such as agents that inhibit LSD1 activity, will be useful to suppress DUX4 and are candidate therapeutic agents for FSHD. Such agents are believed to also have application to other diseases, such as myotonic dystrophy or Huntington's disease, where increasing chromatin mediated suppression of the mutant allele would have therapeutic benefit.

An Agent that Modifies Translation Dependent Nonsense Mediated Decay Will Stabilize DUX4 mRNA Levels

The 3-prime untranslated region (UTR) of the DUX4 mRNA has an unusual exon-intron structure. The translational stop codon is in the first exon, whereas the polyadenylation sequence is in the third exon. The separation of the translational stop codon from the polyadenylation site by two exon-intron junctions would be predicted to make this mRNA subject to translation dependent nonsense mediated decay. The inventors can demonstrate that blocking translation with cycloheximide results in the accumulation of the DUX4 mRNA, whereas washing out the cycloheximide and permitting translation of the accumulated DUX4 mRNA (as evidenced by the activation of DUX4 target genes) results in the rapid degradation of the DUX4 mRNA.

Results showed that the protein synthesis inhibitor cycloheximide (chx) prevents decay of the DUX4 mRNA (FIG. 6). FSHD fibroblasts expressing low amounds of DUX4 mRNA were stably transduced with a beta-estradiol inducible MyoD so that addition of beta-estradiol will convert them to skeletal muscle, which after 96 hours of induction increases the steady-state levels of the DUX4 mRNA and activates expression of the MyoD target Mgn. At 38 hours in differentiation conditions, there is very low abundance of DUX4 mRNA with MyoD induction alone, whereas the addition of chx results in a significant increase in DUX4 mRNA. Washout of the chx results in the rapid loss of the DUX4 mRNA, disappearing between 2 and 8 hrs of washout. The loss of DUX4 mRNA is associated with its translation since the DUX4 target PRAME 1 is induced as the DUX4 mRNA disappears.

Therefore, approaches that block translation dependent nonsense mediated decay can be used to increase DUX4 mRNA and agents that enhance nonsense mediated decay can be used to enhance the degradation of DUX4 mRNA. The latter would be candidate therapies for FSHD.

Summary of Results:

These results demonstrate that an agent known to inhibit the histone demethylase LSD1 suppresses DUX4 mRNA levels. Therefore, agents that increase chromatin mediated repression, such as agents that inhibit LSD1 activity, will be useful to suppress DUX4 and are candidate therapeutic agents for FSHD. Such agents are believed to also have application to other diseases, such as myotonic dystrophy or Huntington's disease, where increasing chromatin mediated suppression of the mutant allele would have therapeutic benefit.

These results also demonstrate that an agent that modifies translation dependent nonsense mediated decay stabilizes DUX4 mRNA levels. Therefore, approaches that block translation dependent nonsense mediated decay can be used to increase DUX4 mRNA and agents that enhance nonsense mediated decay can be used to enhance the degradation of DUX4 mRNA, which provides a candidate therapy for FSHD.

It is further noted, as described above in Example 2, DUX4-s can bind the same sequences as DUX4-fl but does not activate transcription of the same genes. Therefore, DUX4-s functions as an inhibitor of DUX4-fl and can also be used as an inhibitor for FSHD.

Example 7

This Example demonstrates that activation of germline genes in FSHD muscle cells is directly due to the leaky expression of DUX4.

Rationale:

As described in Example 3, the inventors have demonstrated that DUX4 regulates the expression of many genes expressed almost exclusively in the germline, some of which have known functions in meiosis and gametogenesis. As further described in Example 3, the inventors have also found expression of the DUX4-related genes DUXA and DUX1 in the testis, indicating the likelihood of multiple redundant factors. In order to confirm there is a functional link between DUX4 induction and molecular changes in FSHD muscle, the following siRNA knock-down experiment was carried out which demonstrates that the activation of germline genes in FSHD muscle cells is directly due to the leaky expression of DUX4.

Methods:

siRNA Knockdown of DUX4

siRNAs (Dharmacon) targeted to the mature mRNA of DUX4 and a control siRNA against luciferase were used as follows:

(SEQ ID NO: 179) Control siRNA 5′-r(CUUACGCUGAGUACUUCGA)d(TT)-3′ (SEQ ID NO: 180) DUX4 siRNA-1 5′-r(GAGCCUGCUUUGAGCGGAA)d(TT)-3′ (SEQ ID NO: 181) DUX4 siRNA-2 5′-r(GCGCAACCUCUCCUAGAAA)d(TT)-3′ (SEQ ID NO: 182) DUX4 siRNA-3 5′-r(CAAACCUGGAUUAGAGUUA)d(TT)-3′ (SEQ ID NO: 183) DUX4 siRNA-4 5′-r(GAUGAUUAGUUCAGAGAUA)d(TT)-3′

Cultured FSHD myoblasts were transfected in 35 mm dishes with 30 pmol of siRNA using RNAiMAX (Invitrogen) according to manufacturer's recommendations. Following overnight incubation with siRNA complexes, cells were washed and allowed to recover for 12-24 hours in fresh growth media (F10, 20% FBS, 1 μM dexamethasone, 0.01 μg/ml FGF). When confluent, cultures were changed to differentiation media (F10, 1% horse serum, 10 μg/ml each insulin and transferrin,) for 48 hours. RNA was isolated using RNeasy Miniprep Kit (Qiagen), RT and PCR protocols were performed as described in Snider et al. (2010) using primers 1A (SEQ ID NO:164) and 183 (SEQ ID NO:163).

DUX4-fl PCR

Nested DUX4-fl3′ PCR on primary myoblast and muscle biopsies were performed as described in Snider et al., PloS Genet 6, e1001181 (2010). Primers used were 182 forward (SEQ ID NO: 162) and 183 reverse (SEQ ID NO:163) nested with 1A forward (SEQ ID NO:164) and 184 reverse (SEQ ID NO:165).

Dominant Negative Inhibition of DUX4-fl

Cultured FSHD myoblasts were grown to confluence and switched to differentiation media as described above. Simultaneously, cells were transduced by lentivirus carrying DUX4-s or GFP along with 8 μg/mL polybrene. Cells were washed and changed to plain differentiation media after 24 hours. Cells were harvested for RNA after 48 hours of differentiation. Untransduced cells were used to assess baseline expression of DUX4-fl target genes.

Results:

The siRNA sequences that decreased the DUX4-fl mRNA also resulted in decreased expression of the DUX4 target genes, confirming that endogenous DUX4 drives the expression of these genes in FSHD muscle cells.

Results showed that, in a RT-PCR assay, siRNA knockdown of endogenous DUX4-fl in cultured FSHD muscle cells, done in triplicate with Timm17b as an internal standard. Negative control siRNA is against unrelated luciferase gene. Further results showed the results of qPCR analysis of DUX4-fl target genes in the presence of siRNA to endogenous DUX4-fl, relative to the control treated samples, demonstrating that the levels of DUX4-fl target genes were also reduced when endogenous DUX4-fl was knocked down. Error bars represent standard deviation of triplicates, *P<0.05, **P<0.01 between DUX4 siRNA and control siRNA treated cells.

Results of real-time RT-PCR quantitation of three target genes, PRAMEF1 (A), RFPL2 (B) and MBD3L2 (C) in FSHD cultured muscle cells transduced with lenti-GFP or lenti-DUX4-s or untransduced controls were obtained. The abundance of targets was calculated relative to internal standard RPL13a and then set as percentages relative to the untransduced condition. Values represent mean+/−SEM from three independent experiments. DUX4-s blocks expression of these three DUX4-fl target genes in FSHD muscle cells. These results are consistent with the results described in Example 3, demonstrating that expression of the dominant negative DUX4-s also inhibited the endogenous expression of the target genes. These results confirm that the activation of germline genes in FSHD muscle cells is due to the leaky expression of DUX4 in FSHD muscle cells.

Therefore, the results shown in this example demonstrate that agents that inhibit the activity of DUX4, either by eliminating its expression in the muscle cells, as done in vitro with an siRNA, or by introducing a dominant negative agent, such as the DUX4-s splice form are expected to be useful as therapeutic agents for treating and/or preventing FSHD, or symptoms related to FSHD.

Example 8

This Example demonstrates that DUX4-induced DEFB103 inhibits the innate immune response and muscle differentiation.

Rationale:

As described in Example 5, the inventors have determined that genes enriched in the innate immunity pathway were expressed at lower levels in myoblasts transduced with lenti-DUX4 compared to the lenti-GFP or lenti-DUX4-s. When compared to non-transduced cells, it was evident that about 350 genes, as shown in TABLE 11 and as shown in updated TABLE 13 included below, most of which were in the innate immunity pathway, were unchanged in the lenti-DUX4-fl transduced myoblasts but increased in cells transduced with either control lenti-GFP or lenti-DUX4-s. Therefore, lentiviral induction of the innate immune response in human muscle cells appear to be inhibited by DUX4-fl.

In this Example, experiments were carried out to further determine the effects of DUX4-fl induced expression on the innate immunity pathway and the myogenesis pathway.

Methods:

Real time RT-PCR quantitation of innate immune responsive genes and genes involved in muscle differentiation was carried out on lenti-GFP infected cells, lenti-DUX4-fl infected cells and uninfected control cells, as described below.

Beta-Defensin 3 and Innate Immune Response

Cultured control human myoblasts were grown to 80% confluence and infected with equivalent titers of lenti-GFP, lenti-DUX4-s and lenti-DUX4-fl in growth media supplemented with 8 μg/mL polybrene. Expression of innate immune responsive genes including IFIH1 (MDA5), ISG20 and DEFB103 were assessed by real-time qPCR as previously described at 24 hours (primer sequences below). For conditioned media, cells were infected with lenti-DUX4-fl for 12 hours, thoroughly washed 3 times with PBS and switched to fresh growth media to condition for 12 hours. Control conditioned media was produced from cells not infected with any lentivirus. Myoblasts were infected with lenti-GFP in either control conditioned media, lenti-DUX4-fl conditioned media or regular growth media supplemented with 1 μM human β-defensin 3 (Peptides International, Louisville, Ky.). Expression of innate immune responsive genes were examined after 24 hours.

Gene Forward primer Reverse primer name sequence sequence IFIH1 CTAGCCTGTTCTGGGGAAGA AGTCGGCACACTTCTTTTGC (SEQ ID NO: 184) (SEQ ID NO: 185 ISG20 GAGCGCCTCCTACACAAGAG CGGATTCTCTGGGAGATTTG (SEQ ID NO: 186) (SEQ ID NO: 187) DEFB103 TGTTTGCTTTGCTCTTCCTG CGCCTCTGACTCTGCAATAA (SEQ ID NO: 188) (SEQ ID NO: 189)

Beta-Defensin 3 and Muscle Differentiation

Cultured control myoblasts were grown at 50% confluence and treated with 1 μM human β-defensin 3. Equivalent volume of vehicle (water) was added to myoblasts for the control condition. Quadruplicate samples of control- and DEFB103-treated myoblasts were assessed for global expression changes on HumanHT-12 v4 Expression BeadChip Whole Genome arrays and analyzed as described in main methods. Differential expression of myostatin (MSTN) was confirmed by real-time qPCR.

Gene Forward primer Reverse primer name sequence sequence MSTN CTGTAACCTTCCCAGGACCA TCCCTTCTGGATCTTTTTGG (SEQ ID NO: 190) (SEQ ID NO: 191)

Cultured control myoblasts were grown to confluence and switched to differentiation media (as described in Snider et al., 2010). 24 hours later, media was refreshed and either supplemented with 1 μM human β-defensin 3 or equivalent volume of water. Media was refreshed again at 48 hours. Cells were differentiated for a total of 72 hours. Quadruplicate samples were analyzed by expression microarrays as described above. Differential expression of various markers of muscle differentiation were confirmed by real-time qPCR using the primers shown below (see above for CKM and MYH2 primer sequences).

Gene Forward primer Reverse primer name sequence sequence ACTA1 GTACCCTGGGATCGCTGAC CCGATCCACACCGAGTATTT (SEQ ID NO: 192) (SEQ ID NO: 193) CASQ2 AGATTGGGGTGGTGAATGTC TCCTCAATCCAGTCCTCCAG (SEQ ID NO: 194) (SEQ ID NO: 195) TNNT3 CAAGTTCGAGTTTGGGGAGA AGCCTTCTTGCTGTGCTTCT (SEQ ID NO: 196) (SEQ ID NO: 197) MYF6 GCCAAGTGTTTCCGATCATT CACGATGGAAGAAAGGCATC (SEQ ID NO: 198) (SEQ ID NO: 199) DESMIN GATCAATCTCCCCATCCAGA TGGCAGAGGGTCTCTGTCTT (SEQ ID NO: 200) (SEQ ID NO: 201)

Beta-Defensin 3 (DEFB103) and Myotube Formation in Primary Muscle

Cultured primary muscle cells were cultured in differentiation medium for 72 hours in the presence or absence of 0.5 uM Human β-defensin 3. The cells were then immunostained for myosin heavy chain and nuclei, showing that DEFB103 inhibits muscle cell fusion and expression of myosin heavy chain, as compared to the muscle cell cultures that do not contain DEFB103.

As shown in TABLE 13 below, the inventors have determined that genes enriched in the innate immunity pathway were unchanged in the lenti-DUX4-fl transduced myoblasts but increased in cells transduced with either control lenti-GFP or lenti-DUX4-s. Therefore, lentiviral induction of the innate immune response in human muscle cells appears to be inhibited by DUX4-fl.

TABLE 13 Genes induced by lenti-GFP and lenti-DUX4-s but poorly induced by lenti-DUX4-fl GFP v. Short_v. GFP Full v._NoLenti Short_vs. Gene symbol NoLenti (Fc) Full_v. GFP (Fc) (Fc) (Fc) NoLenti (Fc) ABCA1 2.291820276 −1.188123428 −0.317144691 1.103696848 1.974675585 ABI3BP 1.285349969 −1.242569141 −0.399190433 0.042780827 0.886159535 ACSM5 1.171658705 −1.210123921 0.049346191 −0.038465216 1.221004895 ADAR 1.360446453 −2.320782749 0.316391226 −0.960336295 1.676837679 ADAR 1.486951815 −2.180439697 0.356871011 −0.693487882 1.843822826 ADCK3 1.64121942 −1.422215254 −0.173131237 0.219004166 1.468088183 AGAP1 1.390382407 −1.271915967 0.522414096 0.11846644 1.912796503 AGRN 2.630293701 −2.531537554 0.379640013 0.098756147 3.009933713 AK3 1.073902409 −1.251916684 −0.421459526 −0.178014275 0.652442883 ALDH3A2 1.125411852 −1.242892954 −0.194265137 −0.117481102 0.931146715 ALOX15B 1.084246479 −1.214364727 0.715187163 −0.130118248 1.799433642 ANGPT1 1.027654313 −1.084975107 0.217446704 −0.057320794 1.245101017 ANKRA2 1.035862621 −1.17479048 0.327844812 −0.138927859 1.363707433 ANKRA2 1.143001219 −1.343557009 0.246235239 −0.20055579 1.389236458 ANPEP 1.4045147 −2.09404032 0.355618263 −0.689525619 1.760132964 APCDD1 1.816660994 −1.702791884 −0.409640643 0.11386911 1.407020351 APOBEC3G 1.356603191 −1.743348451 1.362079936 −0.38674526 2.718683128 ATL3 1.172765182 −1.43324744 1.336632204 −0.260482258 2.509397386 BATF2 1.051676687 −1.066958424 1.271438373 −0.015281737 2.32311506 BCL3 1.076324149 −1.198088718 −0.043769492 −0.121764569 1.032554657 BCL6 1.239304605 −1.250683236 0.359886105 −0.011378631 1.59919071 BIRC3 1.783961421 −2.14067143 1.056849919 −0.356710009 2.84081134 BST2 4.693875549 −4.110609557 0.211256373 0.583265992 4.905131922 BTG2 1.24201129 −1.524684273 −0.121180138 −0.282672983 1.120831152 BTN3A2 1.396364956 −1.575530186 0.323881527 −0.17916523 1.720246483 BTN3A3 1.342617431 −1.39213812 0.373702947 −0.049520689 1.716320378 C10orf10 2.191627592 −2.507058994 0.142569335 −0.315431402 2.334196927 C14orf159 1.258024351 −1.957895816 0.509946226 −0.699871465 1.767970578 C18orf56 1.451934043 −1.513673871 0.209056629 −0.061739828 1.660990672 C19orf66 1.714465108 −2.178084015 0.603885269 −0.463618907 2.318350377 C1QTNF1 3.514164258 −3.63617124 0.762580688 −0.122006982 4.276744946 C1R 3.431740878 −2.764990793 0.489024106 0.666750085 3.920764984 C1R 4.097498539 −2.991070279 0.476766971 1.10642826 4.574265511 C1RL 1.210460055 −1.453877289 −0.149539045 −0.243417235 1.060921009 C1S 3.50755039 −2.743766253 0.538006932 0.763784136 4.045557322 C4orf34 1.457645505 −1.036411533 0.604138258 0.421233972 2.061783763 C6orf138 1.28233824 −1.176619381 0.946386736 0.105718859 2.228724976 C9orf169 1.550194985 −2.339507952 −0.049415733 −0.789312967 1.500779252 CA12 1.505275285 −2.358845458 0.93380504 −0.853570172 2.439080325 CA9 1.383310651 −1.314316803 0.489105112 0.068993848 1.872415763 CABYR 1.134071595 −1.591154258 −0.041503054 −0.457082663 1.092568541 CCL2 2.390739575 −2.377452771 0.425667754 0.013286804 2.816407329 CCL5 2.46842308 −2.245603872 1.863386716 0.222819207 4.331809795 CCL5 2.792121924 −3.05224536 1.431316683 −0.260123436 4.223438607 CCND2 1.345983368 −1.046404064 −0.528969223 0.299579305 0.817014146 CCND2 1.211684627 −1.010372009 −0.539017483 0.201312618 0.672667144 CD68 2.369427793 −1.085666614 1.175094172 1.283761179 3.544521965 CDK18 1.479105183 −1.409658202 0.55520404 0.069446981 2.034309223 CDKN1A 1.577318436 −2.005503982 0.150353898 −0.428185547 1.727672334 CEBPB 1.316137124 −2.448210379 0.278125966 −1.132073255 1.59426309 CEBPD 2.027652082 −1.536750261 0.1644903 0.490901821 2.192142382 CES2 1.211182709 −2.015465315 0.060436142 −0.804282606 1.271618851 CES2 1.462241013 −1.322576234 0.297278159 0.139664779 1.759519172 CFB 5.389687275 −5.32123731 0.655123952 0.068449966 6.044811228 CFD 1.460205956 −1.09433816 0.241365677 0.365867797 1.701571633 CFLAR 1.173687322 −1.870286111 0.531638717 −0.696598789 1.70532604 CHI3L2 2.883508876 −2.453932636 0.25288949 0.429576241 3.136398366 CIDEC 1.295153579 −1.12502825 −0.027982338 0.17012533 1.267171242 CLDN15 1.762738312 −2.317560734 −0.503444118 −0.554822422 1.259294194 CLMP 1.100423145 −1.139438434 0.02079778 −0.03901529 1.121220924 CMBL 1.779468214 −1.956455153 0.067785064 −0.176986938 1.847253278 COL7A1 1.672860855 −2.086299714 −0.187476705 −0.413438859 1.48538415 COPS8 1.084649605 −1.235003851 0.143856969 −0.150354246 1.228506574 CORO6 1.154149699 −1.09307255 −0.292855728 0.061077149 0.861293971 CSF3 1.306379572 −1.379014306 0.751058681 −0.072634734 2.057438253 CSF3 1.170619642 −1.285172578 0.512509223 −0.114552936 1.683128865 CST3 1.352916208 −1.114340315 0.173115486 0.238575894 1.526031695 CXCL1 3.161742919 −3.2056022 0.199746505 −0.043859282 3.361489423 CXCL2 1.088531774 −1.12427504 0.000297431 −0.035743266 1.088829206 CXCL5 1.796732217 −2.163410121 0.802217283 −0.366677904 2.5989495 CXCL5 2.552762132 −2.7972733 0.752156307 −0.244511169 3.304918439 CXCL6 1.612320374 −1.711616386 0.16209417 −0.099296012 1.774414544 CXCL6 2.889344416 −2.764659712 0.355794239 0.124684703 3.245138655 CYBASC3 1.566585338 −1.92049503 −0.418331779 −0.353909692 1.148253559 CYFIP2 1.388031804 −2.080860129 0.269013837 −0.692828325 1.657045641 CYGB 1.242739213 −1.222078642 0.144472485 0.020660571 1.387211698 CYP26B1 1.557009643 −1.35288291 0.402951144 0.204126733 1.959960788 CYP27A1 1.603224607 −1.558991917 −0.059213982 0.04423269 1.544010625 DCN 1.780361473 −1.557663269 0.260180776 0.222698204 2.040542249 DCN 1.255744448 −1.364162449 0.516581942 −0.108418 1.77232639 DCN 2.535469628 −2.115329344 0.20630244 0.420140284 2.741772068 DDB2 1.065126371 −1.227252657 0.098724876 −0.162126285 1.163851248 DDR2 2.23329097 −2.184044969 0.628165913 0.049246001 2.861456882 DDX58 2.122646261 −2.302586875 0.020336733 −0.179940614 2.142982994 DDX60 1.857459371 −2.114354393 0.440034021 −0.256895022 2.297493392 DDX60L 1.165403911 −1.453009147 0.631525336 −0.287605236 1.796929248 DGKA 1.146131144 −1.731341707 0.097641823 −0.585210562 1.243772967 DGKA 1.538412659 −2.05990981 0.223417083 −0.521497151 1.761829742 DHX58 2.354550923 −2.524320066 0.681738729 −0.169769142 3.036289652 DKK1 2.058791481 −2.299442613 0.466215843 −0.240651132 2.525007325 DRAM1 1.168624381 −1.055889591 −0.358650503 0.112734791 0.809973878 DUSP10 1.052825287 −1.721052291 −0.082362184 −0.668227004 0.970463102 DUSP19 1.515692701 −2.35548253 0.759827653 −0.839789829 2.275520354 EGFR 1.23501357 −1.29432245 1.188755373 −0.05930888 2.423768943 EIF2AK2 2.716902652 −2.268220749 0.552783876 0.448681903 3.269686528 EPSTI1 4.363652437 −4.026958202 0.683321824 0.336694234 5.046974261 ERAP2 1.617866844 −1.564993767 0.765635296 0.052873078 2.38350214 FAM160B1 1.895947832 −1.553397895 1.542319975 0.342549937 3.438267807 FAM198B 1.372529451 −1.749916317 −0.511628689 −0.377386866 0.860900762 FAM198B 1.564969517 −1.666998002 −0.288322282 −0.102028485 1.276647235 FBXO32 2.567095797 −1.157656064 0.762440333 1.409439733 3.32953613 FBXO32 2.993395576 −1.797189568 0.768145422 1.196206008 3.761540997 FILIP1L 1.21285947 −1.72307622 0.063505825 −0.51021675 1.276365295 FKBP5 1.059782793 −1.768400334 −0.105221181 −0.708617541 0.954561612 FOXQ1 1.487355619 −1.213797134 0.586270597 0.273558485 2.073626216 FRMD3 1.264347851 −1.008896541 −0.268549855 0.25545131 0.995797996 FST 1.879306676 −1.797658416 0.915428493 0.08164826 2.79473517 FTH1 1.16763403 −2.003091159 −0.411200627 −0.835457129 0.756433403 FTH1P3 1.578547897 −2.546551924 0.458681522 −0.968004027 2.037229419 FUCA1 1.553243173 −1.53000218 0.284588564 0.023240994 1.837831738 GALNTL2 1.627249768 −1.600577362 0.951168181 0.026672406 2.578417949 GAS1 1.248292919 −1.730183911 0.006982613 −0.481890992 1.255275533 GAS1 1.307924743 −1.545046265 0.089615034 −0.237121521 1.397539777 GBP1 1.663035588 −2.204470258 0.995466771 −0.54143467 2.658502359 GBP1 1.539177456 −1.911140496 1.032949835 −0.37196304 2.572127291 GBP2 2.194934144 −2.389860644 0.677298854 −0.1949265 2.872232998 GBP4 1.335924885 −1.254995665 2.240198911 0.08092922 3.576123797 GDF15 1.771872719 −2.053594964 0.915096518 −0.281722245 2.686969237 GFPT2 1.729215691 −1.590429831 0.049458918 0.13878586 1.778674609 GRINA 1.773238707 −1.404244628 0.466739167 0.368994079 2.239977874 GRINA 1.161955946 −1.198733642 0.421477903 −0.036777696 1.583433849 H1F0 1.210846088 −2.357976468 0.498399795 −1.14713038 1.709245883 HCG4 1.247551934 −1.625383459 0.675501339 −0.377831525 1.923053273 HECW2 1.217292839 −1.048324787 0.055161117 0.168968052 1.272453956 HERC5 5.367300538 −3.156622521 1.346816689 2.210678018 6.714117227 HERC6 3.892685006 −3.57126233 0.518426791 0.321422676 4.411111797 HIPK2 1.273540096 −1.156200641 0.35601076 0.117339455 1.629550856 HLA-A 1.224282572 −1.070849545 0.574982093 0.153433026 1.799264664 HLA-B 3.448509688 −2.752055852 0.333358529 0.696453836 3.781868217 HLA-C 2.043797634 −1.72804812 0.602243193 0.315749513 2.646040827 HLA-E 2.489318232 −1.122898369 0.809237995 1.366419864 3.298556227 HLA-F 1.873709807 −1.735091355 0.913162292 0.138618452 2.786872099 HLA-F 2.704239531 −2.113067715 0.61482352 0.591171816 3.319063051 HLA-G 1.084389593 −1.205707251 0.109199209 −0.121317658 1.193588802 HLA-H 1.297130552 −1.669181838 0.321169353 −0.372051286 1.618299905 HLA-H 2.553573965 −2.193531507 0.353939424 0.360042458 2.90751339 HOXC13 1.000534735 −1.088749573 0.444564824 −0.088214838 1.445099559 IFI16 1.841068311 −1.984982422 0.679092735 −0.143914111 2.520161046 IFI27 7.303388227 −6.379335039 0.300265465 0.924053188 7.603653692 IFI35 3.410532516 −3.729262173 0.92164533 −0.318729656 4.332177846 IFI44 3.287546389 −2.389816265 0.30094931 0.897730124 3.588495698 IFI44L 5.753370016 −5.011530642 0.464189819 0.741839374 6.217559834 IFI6 5.085469725 −4.262101551 −0.040327545 0.823368174 5.04514218 IFIH1 (MDA5) 3.693641619 −3.44578554 1.642722308 0.247856079 5.336363928 IFIT1 4.787387527 −4.356740033 0.716020264 0.430647493 5.503407791 IFIT2 4.365674354 −4.164948286 2.078380504 0.200726068 6.444054859 IFIT3 3.681888585 −3.640974725 1.807701431 0.040913859 5.489590016 IFIT3 5.228105553 −4.765773435 1.104511852 0.462332118 6.332617405 IFIT3 3.365518868 −3.151248319 0.534775341 0.214270549 3.900294209 IFIT5 1.071262503 −1.42655834 −0.257503173 −0.355295837 0.81375933 IFITM1 6.728483235 −5.998523582 0.346633408 0.729959653 7.075116644 IFITM2 1.287202103 −1.750085601 0.0071809 −0.462883498 1.294383003 IFITM3 1.982789092 −1.995925104 −0.140675202 −0.013136012 1.84211389 IGDCC4 1.215267655 −1.594375685 −0.624900224 −0.37910803 0.59036743 IGFBP4 2.222133478 −1.926807782 0.418741062 0.295325696 2.64087454 IGFBP5 1.215794572 −1.28188317 0.168705129 −0.066088598 1.384499701 IGFBP5 1.539901788 −1.310867444 0.281298714 0.229034345 1.821200502 IL18BP 2.005806379 −1.15855931 1.366694726 0.847247069 3.372501105 IL1R1 1.321158201 −1.23340973 0.287796205 0.087748472 1.608954406 IL32 2.025999493 −2.208173565 0.154358881 −0.182174073 2.180358374 IL7R 1.506258978 −1.99732977 0.548115296 −0.491070792 2.054374274 IL8 3.516952055 −3.648099533 1.170200764 −0.131147477 4.687152819 IL8 5.331346339 −5.451111992 0.930533775 −0.119765653 6.261880114 IRAK3 1.353708064 −1.342339713 1.020300119 0.01136835 2.374008182 IRF7 2.864351588 −1.844318439 1.125390895 1.020033148 3.989742483 IRF7 2.755432373 −2.160487542 0.95548081 0.594944831 3.710913184 IRF9 2.42820399 −2.232627679 0.295571895 0.195576311 2.723775884 ISG15 5.06042249 −4.31794577 0.141645299 0.74247672 5.202067789 ISG20 2.30394629 −2.679339661 2.329592064 −0.375393371 4.633538353 ITPRIP 1.1013701 −1.710399371 0.554083786 −0.60902927 1.655453886 KIAA0247 2.303673186 −2.013448857 0.358981191 0.290224329 2.662654377 KLF9 1.023238226 −1.245660536 −0.052040135 −0.22242231 0.971198091 KRT17 1.380656082 −1.409415072 0.431567127 −0.02875899 1.81222321 KYNU 1.119459921 −1.093624095 1.337790233 0.025835826 2.457250155 LAP3 1.749851576 −1.537094669 1.409981585 0.212756907 3.159833161 LGALS3BP 2.681022143 −2.112677157 0.317090182 0.568344986 2.998112325 LNPEP 1.763130709 −1.279670486 2.052682291 0.483460223 3.815813 LTBR 1.168565135 −1.14953269 0.400952848 0.019032446 1.569517983 LUM 1.151065803 −1.112365335 0.386054713 0.038700469 1.537120516 LY6E 3.685056133 −3.242347639 0.257332792 0.442708494 3.942388925 MAMDC2 1.733193514 −1.841626819 −0.027430153 −0.108433305 1.705763361 MAOA 1.417318353 −1.497995721 −0.34587423 −0.080677369 1.071444123 MLKL 1.566078589 −2.71738901 1.443379629 −1.151310421 3.009458218 MME 1.086772749 −1.03372451 −0.182908298 0.053048238 0.903864451 MMP3 1.238760776 −1.286719097 0.258499598 −0.047958321 1.497260374 MMP7 1.284665197 −1.062720937 0.191250354 0.22194426 1.475915551 MOCOS 1.129068005 −1.661858991 0.417460239 −0.532790986 1.546528244 MR1 1.191026064 −1.17841186 0.658029657 0.012614204 1.849055721 MSI2 1.97398629 −1.695161066 1.317806308 0.278825224 3.291792598 MT1F 1.224979554 −1.148897962 −0.529782109 0.076081593 0.695197445 MT1G 1.293754959 −1.240605881 0.255687444 0.053149078 1.549442403 MT1M 2.698286944 −2.872732992 1.198565544 −0.174446049 3.896852488 MT1X 1.981216 −2.450995611 0.310879734 −0.469779611 2.292095734 MTSS1 1.331426508 −1.069633876 −0.39218049 0.261792632 0.939246018 MTSS1 2.167447769 −1.354900669 −0.443277442 0.8125471 1.724170327 MUC1 1.431503927 −1.575675409 0.338131504 −0.144171482 1.769635431 MUC1 1.203764531 −2.101829876 0.322803033 −0.898065345 1.526567564 MUSK 1.324782191 −1.183254592 0.586577408 0.141527599 1.911359599 MX1 7.205558299 −5.623173414 0.288267363 1.582384885 7.493825662 MX2 3.852926817 −3.778486728 0.945818472 0.074440089 4.798745289 MYBPHL 1.409152912 −1.384607359 −0.499125714 0.024545554 0.910027198 NACC2 1.184709948 −1.618000195 0.95658574 −0.433290247 2.141295688 NDRG1 1.630384529 −2.292807858 0.654936282 −0.66242333 2.285320811 NDUFA4L2 1.149943565 −1.122951133 0.177144155 0.026992433 1.32708772 NFE2L2 1.280834247 −1.085476789 0.32469271 0.195357458 1.605526957 NFIL3 1.843454665 −1.768559534 0.321122226 0.074895131 2.16457689 NFKBIA 2.185485916 −3.012569006 0.269962031 −0.82708309 2.455447947 NFKBIZ 1.845887352 −1.544280602 −0.266011822 0.30160675 1.57987553 NRCAM 1.109271808 −1.109495143 −0.100930752 −0.000223335 1.008341055 NTPCR 1.001528266 −1.091034449 0.353533227 −0.089506183 1.355061493 OAS1 4.380499828 −4.254302153 1.43883568 0.126197675 5.819335508 OAS1 3.600570008 −3.699570683 1.298090435 −0.099000675 4.898660443 OAS1 3.760626423 −3.807467129 1.290300518 −0.046840706 5.050926941 OAS2 2.378995669 −2.376411131 0.439887914 0.002584538 2.818883583 OAS2 1.558066832 −1.597321635 0.992880408 −0.039254803 2.55094724 OAS2 5.94172586 −5.520599629 0.386635011 0.421126231 6.32836087 OAS3 3.731806761 −3.817466129 0.853256816 −0.085659368 4.585063577 OASL 1.249672439 −1.117056273 1.634341212 0.132616165 2.884013651 OASL 3.536129109 −3.373570039 2.063311525 0.16255907 5.599440634 PAPPA 1.773861156 −2.036309436 0.390380692 −0.262448279 2.164241848 PARP10 1.326615304 −2.536442296 0.402346977 −1.209826991 1.728962281 PARP12 2.850604542 −3.023002311 0.766021002 −0.172397769 3.616625545 PARP14 2.583199759 −2.668276254 0.521446407 −0.085076495 3.104646166 PARP9 2.126994093 −1.978563435 0.430816142 0.148430659 2.557810235 PARP9 3.27501628 −2.702171197 0.444946635 0.572845083 3.719962915 PCBP3 1.037949803 −1.019127778 0.201291636 0.018822025 1.239241439 PDK4 1.618120933 −1.329005545 0.022234341 0.289115388 1.640355274 PDPN 1.451948088 −1.541326521 −0.284732802 −0.089378433 1.167215286 PHF11 1.569022139 −2.232289429 0.650930764 −0.663267289 2.219952903 PHF11 1.486247098 −2.46187233 0.512439235 −0.975625232 1.998686333 PHLDA3 1.183373039 −1.520391317 0.197956852 −0.337018278 1.381329891 PLA2G4C 1.014228181 −1.304151409 0.071454308 −0.289923228 1.085682489 PLEKHA4 1.637450704 −1.3962661 1.317454769 0.241184604 2.954905473 PLXNB1 1.022415626 −1.365163177 −0.096237354 −0.342747551 0.926178272 PPAP2A 1.209105487 −1.07983494 0.545678749 0.129270547 1.754784236 PRIC285 3.012033847 −2.562869089 0.854090164 0.449164758 3.866124011 PSMB8 1.741409023 −2.133472048 0.71176636 −0.392063025 2.453175382 PSMB8 1.866869714 −2.200415524 0.645884897 −0.33354581 2.512754611 PSMB8 2.084184811 −2.268354645 0.5538343 −0.184169834 2.638019111 PSMB9 2.430860946 −2.965037107 0.939217969 −0.534176161 3.370078914 PSME1 1.487094034 −1.159108877 0.270285521 0.327985157 1.757379556 PSME2 1.33182787 −1.465882921 0.446427126 −0.134055051 1.778254996 PSTPIP2 1.09063831 −1.179957984 0.435242738 −0.089319674 1.525881048 PTGER2 1.000183179 −1.17556292 −0.202348968 −0.175379741 0.797834212 PTGES 1.148907799 −1.41021311 0.290393152 −0.261305311 1.439300951 PTGFR 1.449331827 −1.001601653 0.144372433 0.447730174 1.593704259 PTGFR 1.603159628 −1.169956502 0.207292196 0.433203126 1.810451824 PTX3 2.263730112 −2.441375044 0.922458958 −0.177644932 3.18618907 PYGB 1.107233391 −2.015216504 −0.118331933 −0.907983113 0.988901458 RARRES3 2.25204439 −2.047163548 1.253186958 0.204880842 3.505231348 RBCK1 1.149568733 −1.372120151 0.357340897 −0.222551418 1.50690963 RBM43 1.286746579 −1.355757178 0.307342528 −0.069010599 1.594089107 RCAN1 1.356269615 −2.044901472 0.590666079 −0.688631857 1.946935694 RELB 1.327414196 −1.197089288 0.265979581 0.130324908 1.593393777 RNF213 1.026257639 −1.741511934 −0.290717605 −0.715254295 0.735540034 RSAD2 2.054673683 −2.109763462 2.325557335 −0.055089779 4.380231018 RTN1 1.418819362 −1.193126029 −0.052438051 0.225693333 1.36638131 RTP4 1.880595259 −1.968387483 1.165511333 −0.087792223 3.046106592 S1PR3 2.559224128 −2.033491398 1.123858575 0.52573273 3.683082702 SAA1 3.85141175 −3.821734188 0.256140691 0.029677562 4.107552441 SAA1 1.898438098 −2.092755962 0.278410761 −0.194317864 2.17684886 SAA2 1.037522145 −1.01522487 0.248605491 0.022297274 1.286127636 SAMD9 2.925593069 −2.794870287 1.396975715 0.130722782 4.322568785 SAMD9L 2.369767909 −2.404963489 1.249533389 −0.035195579 3.619301299 SCHIP1 1.175607634 −1.985056899 0.060788621 −0.809449265 1.236396254 SEMA4B 1.085951137 −1.750329849 0.149020906 −0.664378712 1.234972043 SERPINA3 4.119662196 −2.227495953 −0.287856775 1.892166243 3.831805421 SERPINE2 1.442986361 −1.370783037 0.204105894 0.072203324 1.647092255 SERPING1 1.693843482 −1.460555279 1.17423948 0.233288203 2.868082962 SESN1 1.939615386 −1.536312348 −0.112046912 0.403303038 1.827568474 SHISA5 1.977851326 −1.756748253 −0.28305778 0.221103073 1.694793547 SLC15A3 3.130576286 −3.64382322 0.779102407 −0.513246933 3.909678693 SLC22A18 1.2134566 −1.443898771 −0.050527818 −0.23044217 1.162928783 SLC2A5 1.72003983 −1.822730899 0.79755969 −0.102691069 2.51759952 SLC39A14 1.097600298 −1.749617299 0.470029151 −0.652017 1.567629449 SLC39A8 1.244476955 −1.095426078 0.863021155 0.149050877 2.10749811 SLC44A1 1.71490211 −1.104904122 0.779718309 0.609997987 2.494620419 SLC7A11 1.166852082 −1.137370507 1.259609808 0.029481575 2.42646189 SLC7A2 2.259398922 −2.39407 −0.106968828 −0.134671078 2.152430093 SNAI2 1.342068773 −2.049114848 0.214733442 −0.707046075 1.556802215 SOD2 5.212222862 −4.543679151 1.537353539 0.668543711 6.749576401 SOD2 4.995584404 −3.780434297 0.347061658 1.215150107 5.342646062 SOD2 1.60136037 −1.58646149 −0.064257692 0.01489888 1.537102678 SP100 2.100236314 −2.018687379 1.188181794 0.081548935 3.288418108 SP100 1.508601396 −1.642600221 1.176024656 −0.133998825 2.684626052 SP110 2.518950711 −2.846716622 1.137414514 −0.327765911 3.656365225 SP110 1.720088434 −1.882249168 1.055346467 −0.162160733 2.775434901 SP110 2.690392001 −2.892516229 1.103030741 −0.202124228 3.793422743 SP110 1.310024912 −1.487091031 0.740242611 −0.177066119 2.050267523 SPATA18 1.944042704 −1.862961372 −0.20921297 0.081081332 1.734829734 SPTLC3 1.188352855 −1.296558987 0.230797274 −0.108206132 1.419150129 SPTLC3 1.17708351 −1.407741922 −0.378437155 −0.230658412 0.798646355 SRGN 1.075062288 −1.878809962 0.204158948 −0.803747674 1.279221236 SRGN 1.238744661 −1.68310726 0.209977919 −0.444362599 1.44872258 SSBP2 1.005366935 −1.261257011 0.350878869 −0.255890076 1.356245804 SSH2 1.199702614 −1.247618181 −0.311161918 −0.047915566 0.888540696 STAT1 3.947853023 −2.871457346 0.837427127 1.076395677 4.785280151 STAT1 3.99689458 −2.848826485 0.468407551 1.148068096 4.465302131 STAT1 2.906304539 −2.585014232 −0.093155195 0.321290307 2.813149344 STAT2 1.915817586 −2.686061344 0.191027908 −0.770243758 2.106845494 STC1 1.0292146 −1.457999055 0.794608722 −0.428784454 1.823823322 STOM 2.16750243 −2.265579191 0.636207371 −0.098076761 2.803709801 STXBP6 1.685192125 −2.205008349 −0.140264617 −0.519816224 1.544927508 STXBP6 1.357533381 −1.548702316 −1.014370584 −0.191168935 0.343162797 SUSD1 1.167809054 −1.215356084 0.502018478 −0.04754703 1.669827532 SUSD2 1.995586666 −1.30123156 −1.843821737 0.694355106 0.151764929 TAP1 2.554918275 −3.250566846 0.704354101 −0.695648571 3.259272376 TAP2 1.139829115 −1.104732199 1.295486422 0.035096916 2.435315537 TAP2 1.495730318 −1.568017857 −0.063687025 −0.072287539 1.432043293 TAPBP 1.779590119 −1.814839188 0.46938487 −0.035249069 2.248974988 TCEA3 1.187385692 −1.689879617 −0.116757872 −0.502493925 1.07062782 TGFBR3 1.642867893 −1.213035396 0.441813674 0.429832497 2.084681566 TLR3 1.00307105 −1.066022034 1.561205837 −0.062950984 2.564276887 TMEM140 2.60512035 −2.638936113 0.985994997 −0.033815763 3.591115347 TMEM179B 1.063133997 −1.059209078 0.48556917 0.003924918 1.548703167 TNFAIP2 1.009483894 −1.432893589 0.055437207 −0.423409695 1.0649211 TNFAIP3 2.222657286 −2.600109658 0.274980522 −0.377452372 2.497637808 TNFAIP6 3.800322521 −2.175271279 1.295987256 1.625051242 5.096309777 TNFRSF14 1.212245798 −2.570296708 0.566392867 −1.35805091 1.778638665 TNFRSF6B 1.314356831 −1.602258212 0.008270152 −0.287901381 1.322626983 TNFRSF6B 1.045278227 −1.221948387 0.037804436 −0.176670161 1.083082663 TNFRSF6B 1.606266779 −1.778662824 −0.018117171 −0.172396045 1.588149607 TNFSF13B 1.646466367 −1.528604316 2.13086148 0.117862051 3.777327847 TNFSF13B 1.499970062 −1.427861244 2.150984925 0.072108818 3.650954987 TP53I3 1.219126295 −1.936048428 0.187892187 −0.716922133 1.407018482 TP53INP1 1.372265015 −1.110614071 −0.560185532 0.261650944 0.812079483 TRIM21 1.94378019 −1.315572815 0.970781411 0.628207375 2.9145616 TRIM22 2.23643209 −2.500884935 −0.01884083 −0.264452845 2.21759126 TRIM25 2.180788981 −2.44717143 0.507762266 −0.266382449 2.688551247 TRIM5 1.356054889 −1.320968917 1.331111668 0.035085972 2.687166557 TRIM55 1.011150302 −1.049617761 0.204866799 −0.038467459 1.216017102 TSC22D3 1.675169239 −1.64108393 0.195597878 0.034085309 1.870767117 TSC22D3 2.367185894 −1.913270465 0.277087408 0.45391543 2.644273302 TSC22D3 2.253212406 −1.519040364 0.175595871 0.734172041 2.428808277 TTC39B 1.177973441 −1.145548414 1.195730435 0.032425027 2.373703876 TYMP 3.590408302 −4.248591981 0.616829013 −0.658183679 4.207237316 TYMP 1.807874606 −1.828855461 0.992455865 −0.020980856 2.800330471 TYMP 2.13163775 −2.186708951 1.227113406 −0.055071201 3.358751156 TYMP 1.899181412 −1.941140272 0.995147713 −0.04195886 2.894329125 UBA7 1.723362397 −2.412154439 0.569362394 −0.688792042 2.29272479 UBE2L6 2.264152884 −3.092070504 0.57213622 −0.82791762 2.836289104 UBE2L6 1.959635831 −2.107710194 0.942889832 −0.148074363 2.902525663 UGP2 1.152318593 −1.131727121 0.108407345 0.020591472 1.260725938 UNC93B1 1.230652435 −1.872083002 0.936282671 −0.641430567 2.166935106 USP18 2.316759582 −2.22518459 0.972883677 0.091574992 3.289643259 VCAM1 2.680275193 −2.786083447 0.630957412 −0.105808254 3.311232604 VWCE 2.836246852 −3.054134611 −0.118830018 −0.217887759 2.717416834 XAF1 2.657844238 −3.488687703 0.613210061 −0.830843465 3.2710543 XAF1 1.360588979 −1.759772476 0.788471377 −0.399183497 2.149060356 XPC 1.949606716 −2.428503055 0.257466175 −0.478896339 2.207072891 YPEL3 1.246536785 −1.235396214 −0.268728988 0.01114057 0.977807797 ZBTB16 1.972537335 −1.863255579 0.481865817 0.109281756 2.454403152 ZBTB16 1.99291856 −2.195343242 0.412011223 −0.202424682 2.404929783 ZC3H12A 1.664514842 −1.372941613 0.519679139 0.291573229 2.184193981 ZFHX3 1.106012558 −1.699672846 0.50234344 −0.593660287 1.608355998 ZNFX1 1.751304649 −2.100029966 0.809909136 −0.348725317 2.561213785 GFP v. NoLenti (Fc) = log₂ fold change lenti-GFP versus uninfected Full_v. GFP (Fc) = log₂ fold change lenti-DUX4-fl versus lenti-GFP Short_v. GFP (Fc) = log₂ fold change lenti-DUX4-s versus lenti-GFP Full v._NoLenti (Fc) = log₂ fold change lenti-DUX4-fl versus uninfected Short_vs. NoLenti (Fc) = log₂ fold change lenti-DUX4-s versus uninfected

FIGS. 7-11 show the results of real-time PCR analysis demonstrating that DEFB103 inhibits the innate immune response to viral infection and inhibits muscle differentiation. Values shown in FIGS. 7-11 represent mean+/−SD from triplicates and are either expressed as relative to internal standard RPL13a or as a percentage relative to control condition after being normalized to RPL13a.

The RT-qPCR results validated that lenti-GFP, lenti-DUX4-s and multiple other lentivirus constructs induced the innate immune response in myoblasts, whereas similar titers of lenti-DUX4-fl did not (see FIG. 7A, and data not shown). Additionally, supernatant from DUX4-fl infected cells (CM) reduced the induction of these genes by lenti-GFP (see FIG. 8), indicating that a secreted factor induced by DUX4-fl could mediate this suppressive effect.

DUX4-fl robustly induced expression of DEFB103A/B (β-defensin 3) (set forth as SEQ ID NO:178), as shown in FIG. 7B, which has been shown to inhibit the transcription of pro-inflammatory genes in TLR4-stimulated macrophages (Semple et al., 2011). Indeed, addition of DEFB103 peptide also inhibited the induction of the innate immune response to lenti-GFP when added to the muscle cells at the time of infection (see FIG. 8), but did not prevent viral entry and transduction as measured by copies of viral integrants in the genome and levels of GFP mRNA expressed (data not shown). Thus, DUX4 can prevent the innate immune response to viral infection in skeletal muscle cells, at least in part, through the transcriptional induction of DEFB103.

Like other DUX4-regulated genes, endogenous expression of DEFB103 was detected in FSHD cultured muscle cells, FSHD biopsies, and in healthy testes, but little to none was seen in control skeletal muscle, as shown in FIG. 9.

DEFB103 has been previously shown to bind to the CCR6, CCR2, and melanocortin receptors and to be an antagonist ligand for the CXCR4 receptor, which is important for muscle cell migration and differentiation (Candille et al., 2007, Feng et al., 2006; Jin et al., 2010; Yang et al., 1999). To determine whether DEFB103 could affect myoblasts or muscle differentiation, the inventors treated cultured control human muscle cells with DEFB103 peptide at concentrations considered to be physiological (0.5-1.0 ug/ml) (see Midorikawa et al., 2003; Semple et al., 2011), and assessed changes with gene expression arrays. Based on a 2-fold change threshold, DEFB103 did not alter the expression of any genes in myoblasts, although it is of interest that myostatin was upregulated approximately 50% and RT-qPCR confirmed that DEFB103 increased the mRNA for myostatin in myoblasts (as shown in FIG. 11). In contrast, exposing differentiating muscle cells to DEFB103 reduced the expression of 44 genes relative to the untreated control, the majority of which were genes associated with muscle differentiation, as shown below in TABLE 14.

TABLE 14 DEFB103 suppresses the induction of skeletal muscle differentiation genes. Symbol log₂ FC defMT/MT log₂ FC MT/MB ACTA1 −2.65 5.42 MYH8 −2.62 4.58 MYH3 −2.20 6.93 CASQ2 −2.00 3.49 CKM −1.90 3.28 MYL4 −1.86 4.59 SMPX −1.76 2.92 MYH7 −1.73 2.11 CACNG1 −1.58 2.51 TNNT3 −1.55 2.85 MYLPF −1.53 6.54 TNNT3 −1.52 2.89 ENO3 −1.51 3.38 MYBPH −1.49 5.13 TNNC2 −1.49 2.29 LOC389827 −1.48 2.30 ENO3 −1.47 2.51 TNNC1 −1.45 5.92 TPM2 −1.41 3.53 HRC −1.40 3.31 LOC389827 −1.38 2.20 HES6 −1.24 3.80 VASH2 −1.22 1.78 MYOM1 −1.20 1.70 MYL1 −1.18 5.71 AIF1L −1.16 1.95 CKB −1.16 2.98 CTGF −1.12 0.82 MYL1 −1.11 5.58 HBEGF −1.10 2.07 PRAGMIN −1.10 1.38 FOLR1 −1.10 1.45 ZFP106 −1.09 1.55 MYL4 −1.08 1.98 SMYD1 −1.07 2.42 ARPP-21 −1.06 2.86 CYP2J2 −1.05 1.39 ATP2A2 −1.04 2.48 HFE2 −1.04 2.89 RASSF4 −1.03 2.49 IL32 −1.03 1.85 FOLR1 −1.03 1.38 LMCD1 −1.03 1.24 MYL6B −1.00 1.59 TNNT1 −1.00 2.27 NDRG1 1.01 −0.09 ANGPTL4 1.21 −0.76 DKK1 1.22 −3.56 MME 1.27 −1.36 AKR1C2 1.41 2.32 PLIN2 1.61 −0.76 MT1X 1.65 −1.50 HMOX1 1.66 −0.15 PLIN2 1.79 −0.93

-   -   log 2 FC DefMT/MT is the log 2 ratio of expression in DEF103         treated muscle cells compared to control muscle cells     -   log 2 FC MT/MB is the log 2 ratio of expression in         differentiated muscle cells to myoblasts

As shown in FIG. 11, RT-qPCR on select genes (ACTA1, CKM, CASQ2, MYH2 and TNNT3) validated the array results. Therefore, DEFB103 activates the expression of myostatin in myoblasts and inhibits the expression of genes necessary for normal muscle differentiation. Therefore, DUX4-mediated expression of DEFB103 in FSHD muscle can modulate the innate immune response to retroviral infection and can inhibit myogenic differentiation.

The induction of DEFB103 by DUX4 might influence both the adaptive and the innate immune response. DEFB103 can have a pro-inflammatory role in the adaptive immune response and can act as a chemo-attractant for monocytes, lymphocytes and dendritic cells (Lai and Gallo, 2009). In this regard, it might enhance an adaptive immune response to germline antigens expressed in FSHD muscle. Though traditionally known for its role in antimicrobial defense (Sass et al., 2010), DEFB103 has been shown to suppress the innate immune response to LPS and TLR4 stimulation in macrophages (Semple et al., 2011; Semple et al., 2010). DEFB103 has also been shown to be an antagonistic ligand of the CXCR4 receptor (Feng et al., 2006), which is important for muscle migration, regeneration, and differentiation (Griffin et al., 2010; Melchionna et al., 2010).

Discussion of Results

As described herein, the inventors have identified genes regulated by DUX4-fl and show that they are expressed at readily detectable levels in FSHD skeletal muscle, both cell lines and muscle biopsies, but not in control tissues, providing direct support for the model that misexpression of DUX4-fl is a causal factor for FSHD. The genes regulated by DUX4-fl suggest several specific mechanisms for FSHD pathophysiology.

In the Examples provided herein the inventors have demonstrated that DEFB103 inhibited the innate immune response to lentiviral infection in skeletal muscle cells, modestly induced myostatin in myoblasts, and impaired muscle cell differentiation. Therefore, while not wishing to be bound by any particular theory, DEFB103 may contribute to FSHD pathology by modulating the adapative and innate immune response, as well as through inhibiting muscle differentiation.

Reactivation of retroelements can result in genomic instability (Belancio et al., 2010) and transcriptional deregulation (Schulz et al., 2006). Therefore, DUX4 activation of MaLR transcripts might directly contribute to FSHD pathophysiology. It is interesting that DUX4 both activates retroelement transcription and suppresses the virally induced innate immune response. Although the inventors have shown that DEFB103 can substitute for DUX4 to suppress the innate immune response, products of retroelements and endogenous retroviruses may do the same and, thus, the DUX4-mediated suppression of the innate immune response might be multi-factorial. Since DEFB103 is also expressed in the testis, it is interesting to consider whether the role of DUX4 in the germline might include a simultaneous activation of retroelement transcription and suppression of the innate immune response to those transcripts.

DUX4 regulated targets also include genes involved in RNA splicing, developmentally regulated components of the Pol II transcription complex, and ubiquitin-mediated protein degradation pathways, all of which may have pathophysiological consequences. For example, DUX4 is known to induce apoptosis and inhibit myogenesis in muscle cells In this regard, other genes have been identified as candidates for FSHD. For example, FRG1 expression has been reported to be elevated in FSHD muscle (Gabellini et al., 2002) and FRG1 transgenic mice display a muscular dystrophy phenotype (Gabellini et al., 2006). It is interesting the FRG1 is reported to alter RNA splicing in FSHD muscle (Gabellini et al., 2006 supra) and that the inventors' study shows that DUX4-fl also alters the expression of many genes that regulate splicing and RNA processing. It will be important to determine the relative contributions of DUX4 and FRG1 to FSHD pathophysiology; however, the human genetics shows a convincing linkage to polymorphisms necessary for the polyadenylation of the DUX4 mRNA (Lemmers et al., 2010), indicating that DUX4 mRNA is a necessary component of the disease. Therefore, agents that reduce the activity of DUX4, either by eliminating its expression in the muscle cells as the inventors have done in vitro with an siRNA or by introducing a dominant negative, such as the DUX4-s splice form are believed to be useful as therapeutic agents for treatment of subjects suffering from FSHD and/or for prevention of symptoms related to FSHD.

In conclusion, these data support the model that inappropriate expression of DUX4 plays a causal role in FSHD skeletal muscle pathophysiology by activating germline gene expression, endogenous retrotransposons, and suppressors of differentiation in skeletal muscle. The set of genes robustly upregulated by DUX4 in FSHD skeletal muscle are candidate biomarkers because they are absent in control muscle and easily detected in FSHD1 and FSHD2 muscle. Furthermore, some target genes encode secreted proteins, which offer the potential for developing blood tests to diagnose FSHD or monitor response to interventions. Beyond their utilities as candidate biomarkers, the DUX4 targets identified in this study point to specific mechanisms of disease and may help guide the development of therapies for FSHD.

Accordingly, in view of the data demonstrating that DEFB103 blocks myogenesis, the therapeutic indication would be to neutralize or block DEFB103 in FSHD. Therefore in some embodiments, the invention provides DEFB103 inhibitory agents and methods of using DEFB103 inhibitors to treat FSHD subjects and to ameliorate or prevent symptoms associated with FSHD by promoting muscle regeneration/differentiation.

In another embodiment, the invention provides methods of treating a subject suffering from a sarcopenias or other muscular dystrophy by administering an amount of DEFB103 inhibitory agent effective to facilitate normal muscle regeneration/differentiation.

Example 9

siRNA knock-down of UPF1 results in an increase of DUX4 mRNA and an increase in the expression of a DUX4 target gene ZSCAN4. Consistent with the higher DUX4 mRNA in cells with UPF1 knock-down, there is a higher abundance of the ZSCAN4 target gene in the cells with the DUX4 knock-down (FIG. 12A-12B).

Method for transfection of myoblasts with siUPF1 (siRNA against UPF1): Human FSHD myoblasts were plated for transfection at 30% confluency in F10 media containing 20% FBS and no antibiotics. siRNA targeting siUPF1 (ThermoScientific) was transfected at 100 nM final concentration using Lipofectamine 2000 according to manufacturers protocol. siLuciferase was used as a negative control. Following overnight incubation of cells with transfection complexes the cells were washed with PBS and fed fresh growth media: F10 media, 20% FBS, dexamethasone (1 uM) and fgf (10 ng/ml). When cultures reached confluency growth media was replaced with serum free differentiation media (F10 media, insulin and transferrin at 10 ug/ml each) and culture continued for 48 hours. Total RNA was isolated using Qiagen RNeasy columns and analysis for expression of Dux4 mRNA and for target gene activation was performed.

The sequence of siUPF1 used herein is GAUGCAGUUCCGCUCCAUUUU (sense) (SEQ ID NO:202) (See Kim et al.). The cDNA sequence of human UPF1 is NM_(—)002911 (SEQ ID NO:203).

APPENDIX TABLE 1: Expression Array Analysis of DUX4-fl and DUX4-s in cultured human skeletal muscle Symbol Refseq* Full.fc Short.fc Full.pval Short.pval Full.fdr Short.fdr 1. RFPL1S NR_002727.1 8.395820858 0.114675803 4.68E−27 0.239049748 0 0.42494 2. LOC643263 XR_016355.1 8.345299826 −0.13296007 5.16E−27 0.174365432 0 0.34164 3. RFPL4B NM_001013734.2 8.340345819 −0.10307784 5.13E−28 0.233239884 0 0.41777 4. LOC390031 XM_372343.1 8.330613566 −0.10971721 5.02E−28 0.204581737 0 0.38176 5. ZSCAN4 NM_152677.1 8.321990102 0.04366422 1.94E−28 0.589332902 0 0.75086 6. LOC340970 XR_038494.1 8.315993278 0.03296229 3.20E−28 0.69048443 0 0.82273 7. LOC136157 XM_069743.3 8.298510216 0.05270893 1.98E−27 0.561916557 0 0.73064 8. LOC643445 XR_038080.1 8.249957558 0.078820982 1.44E−28 0.322618619 0 0.51927 9. LOC729458 XM_001130308.2 8.246687197 0.008125932 2.30E−27 0.928539738 0 0.96551 10. LOC653192 XM_926437.2 8.228018909 −0.03931919 2.48E−27 0.665571629 0 0.80599 11. LOC645669 XM_928680.1 8.202022481 0.087540869 1.85E−27 0.331908052 0 0.52852 12. LOC391769 XM_001713901.1 8.189552468 0.151962984 3.39E−27 0.109385798 0 0.24599 13. LOC196120 XM_114987.3 8.178925427 0.051907662 2.42E−27 0.566127782 0 0.73383 14. LOC651308 XM_940443.1 8.168661444 0.039056723 4.84E−25 0.740883199 0 0.85586 15. RFPL3 NM_001098535.1 8.144474769 −0.06033097 9.29E−29 0.430802078 0 0.62198 16. PRAMEF1 NM_023013.1 8.072400408 0.069102721 3.19E−27 0.44691755 0 0.63632 17. LOC100134199 XM_001719549.1 8.048036849 0.032523272 6.76E−28 0.695970658 0 0.82645 18. SPRYD5 NM_032681.1 8.044967325 −0.07701669 5.44E−28 0.353686738 0 0.55026 19. LOC284428 XM_208203.5 8.022522551 −0.09940864 1.38E−26 0.309802653 0 0.50524 20. LOC642362 XM_925891.1 8.015825025 −0.01469809 1.66E−27 0.865315092 0 0.92997 21. KHDC1L NM_001126063.2 8.012411091 −0.07068267 1.06E−27 0.407798804 0 0.60161 22. LOC653656 XM_928688.3 7.897231482 −0.14187285 5.40E−28 0.090015441 0 0.21361 23. TRIM48 NM_024114.2 7.880137061 −0.07953563 5.54E−26 0.438422117 0 0.62889 24. LOC653657 XM_928697.2 7.856575803 0.186023041 3.03E−27 0.044025347 0 0.12468 25. PRAMEF12 NM_001080830.1 7.801903788 0.126872497 1.84E−25 0.244937761 0 0.43179 26. LOC441584 XM_497258.1 7.781378819 −0.14419106 4.75E−27 0.115629739 0 0.25615 27. LOC730974 XR_037751.1 7.715075519 0.023836761 9.06E−26 0.815803599 0 0.90182 28. PRAMEF7 NM_001012277.1 7.631155888 0.106015999 1.22E−27 0.201113017 0 0.37739 29. MBD3L2 NM_144614.2 7.622770725 0.026835566 3.46E−26 0.780460765 0 0.88063 30. LOC440040 XM_495873.4 7.533852122 0.081279966 2.79E−27 0.336680469 0 0.53366 31. CCNA1 NM_003914.2 7.525825564 1.883773429 1.10E−26 4.89E−15 0 0 32. PRAMEF13 XM_001713933.1 7.421574077 0.11785555 3.37E−27 0.166851976 0 0.33175 33. LOC342900 XM_001129035.1 7.391093477 0.131534159 4.53E−28 0.090162105 0 0.21383 34. LOC340096 XM_293943.2 7.38245832 −0.07892668 9.80E−25 0.477985391 0 0.66308 35. PRAMEF5 NM_001013407.1 7.34950535 0.105404705 3.80E−23 0.430635599 0 0.62189 36. RFPL2 NM_006605.1 7.293384138 0.031224439 3.38E−25 0.762925317 0 0.87012 37. PRAMEF9 NM_001010890.1 7.130773908 −0.07265342 7.31E−25 0.49226852 0 0.67472 38. LOC100134006 XM_001725030.1 7.08721139 −0.02089226 7.77E−27 0.801081744 0 0.89304 39. PRAMEF4 NM_001009611.1 7.060257208 0.042304869 2.65E−24 0.704169906 0 0.83172 40. PRAMEF15 XM_001713659.1 7.000221925 −0.05867233 4.98E−26 0.516703891 0 0.69394 41. LOC100131392 XM_001713681.1 6.975776511 −0.00710376 9.12E−25 0.945565419 0 0.97352 42. NP NM_000270.1 6.960976026 0.227948457 4.12E−27 0.008382197 0 0.0338 43. LOC399939 XM_374919.3 6.930795087 −0.06731419 9.92E−27 0.415983247 0 0.60893 44. LOC642148 XR_019607.1 6.85089804 0.135198137 8.92E−25 0.1950279 0 0.36981 45. LOC729384 NM_001105522.1 6.831960625 −0.07068137 2.20E−27 0.350703268 0 0.54712 46. ZNF705A NM_001004328.1 6.831813353 −0.0605928 3.44E−27 0.432743467 0 0.6236 47. C6orf148 NM_030568.2 6.759160491 −0.10455994 7.93E−25 0.302878889 0 0.49795 48. TRIM49 NM_020358.2 6.551062725 −0.01702844 3.44E−26 0.836826254 0 0.91386 49. DEFB103A NM_001081551.2 6.441860402 0.065810955 1.15E−25 0.449659752 0 0.63905 50. PRAMEF2 NM_023014.1 6.439143984 −0.04937285 2.12E−25 0.581121856 0 0.74436 51. RFPL1 NM_021026.2 6.264001827 0.340220484 8.17E−25 0.001422993 0 0.00774 52. LOC100133984 XM_001723079.1 6.203778673 −0.03264954 8.08E−25 0.722972189 0 0.84364 53. LOC642127 XM_936272.2 6.112037689 0.04198888 6.46E−24 0.677564423 0 0.81389 54. CA2 NM_000067.1 6.091135387 0.104613634 5.91E−24 0.302024566 0 0.49727 55. PRAMEF10 NM_001039361.1 6.063554254 0.008756171 1.77E−23 0.933700957 0 0.96831 56. LOC646698 XM_929644.2 6.012022368 0.110541637 9.84E−24 0.28229693 0 0.47595 57. LOC729516 XR_038445.1 5.954919316 −0.00368993 1.03E−25 0.96294883 0 0.98328 58. PRAMEF11 XM_001714028.1 5.93984508 0.12170361 1.97E−24 0.196313298 0 0.37122 59. CSAG3 NM_001129826.1 5.871224381 0.090735156 6.50E−24 0.354078253 0 0.55061 60. PRAMEF6 NM_001010889.2 5.82553958 −0.06188677 8.31E−25 0.477094509 0 0.6623 61. LOC391764 XM_373076.3 5.820931052 0.121080051 1.05E−24 0.176502333 0 0.34469 62. TRIM43 NM_138800.1 5.805862854 0.023851911 1.43E−20 0.866762315 0 0.93058 63. LOC391742 XM_373056.1 5.733140049 0.159640297 1.50E−25 0.051475695 0 0.14059 64. LOC391766 XM_373077.2 5.723821554 −0.05536847 3.38E−25 0.497562687 0 0.67933 65. ZNF296 NM_145288.1 5.536035027 0.1758227 9.82E−25 0.044329889 0 0.12539 66. SLC34A2 NM_006424.2 5.513611409 −0.03230882 5.77E−22 0.777899548 0 0.87914 67. LOC391767 XM_373078.1 5.491772222 0.055424445 3.46E−21 0.658195002 0 0.80141 68. LOC729368 XM_001130065.2 5.416246795 −0.0600205 1.19E−23 0.517110941 0 0.69425 69. LOC440563 NM_001136561.1 5.312436177 0.070512689 3.77E−22 0.515651476 0 0.69305 70. LOC646754 XM_929704.2 5.110280465 −0.14855706 3.49E−22 0.161275857 0 0.32367 71. LOC654101 XM_939354.1 5.033863949 0.094787028 5.71E−21 0.42384468 0 0.61572 72. LOC729731 XM_001131140.1 5.007248294 0.098807532 1.46E−23 0.258865952 0 0.44828 73. HIST2H3A NM_001005464.2 4.94502277 −0.05202979 2.03E−21 0.6356191 0 0.78508 74. TRIM64 XM_061890.11 4.943161345 −0.17396551 2.26E−23 0.056348789 0 0.15062 75. LOC402207 XM_377884.2 4.902732221 −0.01834074 6.85E−23 0.840730236 0 0.91594 76. LOC729700 XM_001131081.1 4.817202768 −0.18404267 1.04E−23 0.033176571 0 0.10016 77. LOC645558 XM_928577.2 4.802893457 −0.04868182 1.18E−22 0.597603188 0 0.75758 78. LOC642219 XM_936370.2 4.798732171 4.39E−05 2.95E−20 0.999712853 0 0.99985 79. PRAMEF20 NM_001099852.1 4.795165678 −0.00363174 1.03E−23 0.964219718 0 0.98388 80. HBA1 NM_000558.3 4.786546251 0.080655575 5.55E−23 0.365066949 0 0.56113 81. TRIM53 XR_041244.1 4.777537744 0.079134921 1.16E−22 0.390798501 0 0.58576 82. LOC399940 NM_001136118.1 4.726731116 −0.03723776 6.54E−22 0.70656513 0 0.83286 83. HBA2 NM_000517.3 4.720819569 0.093332131 4.76E−24 0.231860599 0 0.41599 84. LOC646103 XM_377879.3 4.658033426 −0.13870545 6.41E−21 0.214084076 0 0.39391 85. LOC732393 XR_015873.1 4.637178107 0.036830325 1.36E−21 0.714721227 0 0.8384 86. LOC100133446 XM_001717965.1 4.634628768 0.116130356 4.84E−23 0.180518364 0 0.3498 87. LOC100131539 XM_001724873.1 4.629058602 0.065239114 6.67E−21 0.551165724 0 0.72228 88. C12orf50 NM_152589.1 4.521768101 −0.0213687 6.50E−23 0.799126907 0 0.89218 89. OR2T34 NM_001001821.1 4.519029057 −0.05407982 5.05E−23 0.515865558 0 0.69307 90. TPRX1 NM_198479.2 4.483209754 −0.0501894 1.10E−23 0.51112799 0 0.68941 91. LOC402199 XM_377875.2 4.392490269 0.081696113 3.01E−21 0.414457022 0 0.60764 92. LOC646066 XM_116384.2 4.39124129 −0.02686057 2.75E−21 0.785823472 0 0.88355 93. ART3 NM_001179.3 4.363323034 0.090732461 2.34E−22 0.300700573 0 0.49596 94. RFPL4A XM_001719234.1 4.347531657 −0.09031651 6.99E−22 0.327678483 0 0.52442 95. LOC401860 XM_377445.3 4.272236536 −0.13415173 3.19E−21 0.176085184 0 0.34414 96. NXF1 NM_006362.4 4.233044352 −0.34555942 3.92E−22 0.000626159 0 0.00389 97. LOC729706 XM_001131091.1 4.227191316 −0.01625531 1.26E−21 0.858756767 0 0.92628 98. PRAMEF17 XM_938420.2 4.223085794 0.10076379 5.13E−20 0.366524268 0 0.56217 99. SFRS2B NM_032102.2 4.2153031 −0.33354085 3.27E−22 0.000767866 0 0.00463 100. RN5S9 NR_023371.1 4.191231411 0.761555557 9.29E−23 5.90E−09 0 0 101. PPP2R2B NM_181677.1 4.130027648 −0.10914388 1.09E−21 0.226560435 0 0.40935 102. ZNF217 NM_006526.2 4.113561121 −0.32621866 6.85E−22 0.001060723 0 0.00605 103. ENTPD8 NM_001033113.1 4.072927263 0.035234049 1.36E−21 0.690580498 0 0.82277 104. LOC647827 XR_018213.1 4.053399058 −0.05208092 4.92E−20 0.623450204 0 0.777 105. THOC4 XM_001134346.1 4.034801354 −0.18956718 7.79E−22 0.035528484 0 0.10552 106. LOC729694 XM_001131061.1 4.028728476 −0.16550591 2.38E−19 0.157362785 0 0.31828 107. LOC440053 NM_001039615.1 3.918817013 −0.09981524 3.01E−21 0.267252236 0 0.45861 108. LOC440041 XR_018122.2 3.89480714 0.021004094 2.00E−20 0.82868932 0 0.90915 109. HBEGF NM_001945.1 3.868092908 −0.07673133 1.21E−20 0.417643656 0 0.61029 110. NEUROG2 NM_024019.2 3.85681225 −0.00447299 1.25E−21 0.957178138 0 0.98027 111. PANX2 NM_052839.2 3.830560921 0.200055177 8.49E−21 0.03839939 0 0.11233 112. ZNF280A NM_080740.3 3.797765728 0.058889453 4.98E−21 0.506083159 0 0.68592 113. LOC647366 XR_018122.1 3.783001088 −0.00333941 1.25E−21 0.967398855 0 0.98544 114. LOC285697 XM_210642.1 3.782783592 −0.06561338 2.08E−19 0.539118315 0 0.71238 115. LOC441081 XR_017029.1 3.763514442 0.060234864 6.90E−20 0.548451457 0 0.71998 116. LOC342933 XM_938208.2 3.75200974 −0.10207234 4.43E−21 0.246101014 0 0.43311 117. EGR1 NM_001964.2 3.748663671 0.026507346 1.16E−21 0.7427747 0 0.85686 118. DYNC2H1 NM_001080463.1 3.721145052 0.045575817 2.77E−21 0.587582811 0 0.74952 119. LOC100128202 XM_001723719.1 3.711047498 −0.11569545 8.83E−20 0.254283291 0 0.44265 120. PRAMEF8 NM_001012276.1 3.701296487 0.166197201 1.17E−19 0.111383935 0 0.24918 121. SIAH1 NM_001006610.1 3.699147241 −0.07930283 9.21E−22 0.319519563 0 0.51575 122. FLJ45337 NM_207465.1 3.685113625 −0.24611487 1.92E−21 0.006220997 0 0.02649 123. HSPA2 NM_021979.3 3.669897207 −0.25459401 5.26E−20 0.014415927 0 0.05203 124. ODC1 NM_002539.1 3.657122126 −0.2007912 1.71E−21 0.019930626 0 0.06739 125. LOC730167 XM_001726158.1 3.655888029 1.256728305 1.22E−19 6.08E−11 0 0 126. FAM90A1 NM_018088.3 3.636367832 0.029370652 6.18E−19 0.786076088 0 0.88361 127. LOC653194 XM_926449.1 3.632643404 −0.01762031 2.57E−18 0.879603109 0 0.93741 128. PNMA6B XM_001721351.1 3.603031443 −0.2188711 2.19E−18 0.067120975 0 0.17186 129. LOC100132564 XM_001713808.1 3.588075831 0.401019931 1.43E−18 0.001646443 0 0.00875 130. PRR4 NM_001098538.1 3.562468474 0.160622534 7.87E−22 0.042850318 0 0.12235 131. LOC653978 XM_937424.1 3.553895481 0.192785536 1.85E−19 0.063485858 0 0.16471 132. HSPA1A NM_005345.4 3.540028117 −0.02035008 2.76E−18 0.858054237 0 0.92574 133. LOC729698 XM_001131072.1 3.538584507 −0.06572337 1.83E−19 0.508304015 0 0.68753 134. ZNHIT6 NM_017953.2 3.518983721 0.326535866 2.16E−21 0.000424269 0 0.00281 135. NT5C1B NM_001002006.1 3.495396607 −0.03655421 1.38E−19 0.704367331 0 0.83172 136. HNRNPCL1 NM_001013631.1 3.484393042 −0.10353966 2.55E−19 0.302153912 0 0.49734 137. CTGLF7 XM_001714786.1 3.436721543 −0.29494408 3.42E−21 0.001095911 0 0.00621 138. HSPA1B NM_005346.3 3.401785142 0.358980336 4.90E−19 0.001676423 0 0.00889 139. SLC2A3 NM_006931.1 3.385403683 0.101237382 2.04E−20 0.238786567 0 0.42467 140. DBR1 NM_016216.2 3.378534844 0.224692341 7.63E−19 0.036759428 0 0.10848 141. KLHL15 NM_030624.1 3.37342888 0.774243223 9.49E−22 8.73E−10 0 0 142. LOC650167 XM_939249.1 3.363320722 0.048105363 7.07E−21 0.546500283 0 0.7183 143. LOC100130652 XM_001719052.1 3.330216691 0.105014512 2.71E−19 0.275804678 0 0.46865 144. SPTY2D1 NM_194285.2 3.286224106 −0.2916034 4.47E−21 0.000918981 0 0.00538 145. SDHALP1 NR_003264.1 3.276271252 0.122529763 1.06E−20 0.132047058 0 0.28079 146. FBXO33 NM_203301.1 3.219913773 0.216167119 1.72E−19 0.02415313 0 0.07857 147. GTF2F1 NM_002096.1 3.207918515 0.290008826 7.38E−21 0.000980706 0 0.00568 148. FAM90A7 NM_001136572.1 3.19857361 −0.21371846 4.16E−17 0.082629899 0 0.20087 149. TFIP11 NM_012143.2 3.191115229 0.112444499 5.78E−21 0.142573457 0 0.29687 150. PRAMEF14 NM_001099854.1 3.185645753 −0.16938858 1.23E−17 0.136924741 0 0.28794 151. JUP NM_002230.1 3.172493972 −0.10574784 8.62E−19 0.277847276 0 0.47091 152. RAB6B NM_016577.3 3.170174833 0.007069344 1.31E−17 0.948962003 0 0.97536 153. CLDN14 NM_012130.2 3.147780532 −0.3005501 1.06E−20 0.000705891 0 0.00431 154. LOC653111 XM_926073.2 3.139215982 −0.09966257 5.28E−18 0.345009515 0 0.54173 155. FGFR3 NM_022965.1 3.111910187 0.041474475 7.15E−20 0.617422726 0 0.77246 156. LOC642446 XM_001717781.1 3.10134434 0.187941596 2.37E−18 0.068762031 0 0.17497 157. LOC649330 XM_001723218.1 3.10126304 −0.26972993 1.95E−17 0.022495581 0 0.07403 158. SOX9 NM_000346.2 3.099073039 −0.30863513 1.41E−20 0.000545661 0 0.00347 159. KBTBD8 NM_032505.1 3.075609437 0.010765435 5.01E−18 0.915890843 0 0.95951 160. LOC727828 XR_015137.1 3.053539854 −0.00555958 5.39E−20 0.944623917 0 0.97324 161. PPP1R14C NM_030949.2 3.048726581 −0.01369375 8.26E−18 0.894960188 0 0.94666 162. LOC729724 XM_001131132.1 3.038453461 0.111242726 8.02E−20 0.18128368 0 0.35074 163. LOC652433 XM_941875.1 3.022406734 −0.03197171 1.82E−17 0.765570805 0 0.87176 164. LOC391761 XM_373073.2 3.009217657 −0.05893793 4.67E−18 0.554866398 0 0.7253 165. IFRD1 NM_001550.2 2.990137587 −0.19198734 9.17E−19 0.044831594 0 0.12646 166. LOC342934 XM_292724.5 2.987840631 −0.06004995 1.28E−16 0.609711079 0 0.7666 167. DBNDD2 NM_001048223.1 2.986531035 0.225696775 1.48E−19 0.011894374 0 0.04467 168. MGC61598 XM_939432.1 2.969400698 0.095811933 5.41E−19 0.281754516 0 0.47532 169. CSE1L NM_177436.1 2.936775247 0.072869191 3.16E−19 0.392112884 0 0.58683 170. NEFM NM_005382.1 2.92509738 0.848466864 8.17E−18 4.02E−08 0 0 171. LOC650236 XR_036872.1 2.915370575 −0.05944742 1.48E−17 0.562576956 0 0.73099 172. LOC100130311 XM_001724111.1 2.912233006 0.143640536 7.08E−19 0.111098741 0 0.24867 173. EOMES NM_005442.2 2.897434573 0.064838479 8.70E−20 0.409051786 0 0.60273 174. LOC645373 XM_928412.1 2.89149778 −0.06601509 1.86E−16 0.569921908 0 0.73685 175. PELI1 NM_020651.2 2.885705123 0.148281618 3.32E−18 0.124626886 0 0.26982 176. LOC285299 XM_936463.2 2.839952293 −0.03457605 4.43E−17 0.743286409 0 0.85714 177. LOC652349 XM_941777.1 2.835445356 0.016964784 6.30E−17 0.87431718 0 0.93496 178. LOC400464 XR_041115.1 2.831055937 −0.07853086 2.32E−18 0.388228712 0 0.58348 179. LOC391747 XM_373059.2 2.788628167 −0.10487233 8.75E−20 0.172080374 0 0.33855 180. BAMBI NM_012342.2 2.783131683 0.110053957 6.13E−19 0.193134544 0 0.36739 181. PELI2 NM_021255.2 2.782423319 −0.37316879 9.34E−18 0.000780669 0 0.00469 182. T1560 NM_199048.1 2.769356823 0.02012096 1.01E−16 0.851350752 0 0.92166 183. KCNH4 NM_012285.1 2.748842971 −0.07365183 8.94E−17 0.489289998 0 0.67248 184. AMACR NM_014324.4 2.743048821 0.084305604 4.20E−18 0.35465387 0 0.55115 185. SLC3A1 NM_000341.2 2.73626768 0.003792308 7.66E−19 0.963231713 0 0.98339 186. DYNLL2 NM_080677.1 2.735918959 0.652116243 2.47E−17 1.75E−06 0 3.00E−05 187. LOC642843 XM_926241.2 2.72784969 −0.0584813 7.41E−17 0.575540743 0 0.74024 188. LOC100129053 XM_001718702.1 2.724096232 0.0995082 1.76E−17 0.308376623 0 0.50373 189. CCNJ NM_019084.2 2.694767424 0.079155108 2.77E−18 0.365798327 0 0.56146 190. BZW2 NM_014038.1 2.677197026 −0.4002905 5.61E−19 5.53E−05 0 5.00E−04 191. CWC15 NM_016403.3 2.643111234 0.09338116 3.88E−18 0.287130937 0 0.48154 192. CD24 NM_013230.2 2.623896274 −0.35857296 9.32E−18 0.000655138 0 0.00405 193. C9orf61 NM_004816.2 2.614048685 −0.256295 1.47E−16 0.020853562 0 0.06978 194. DENND2C NM_198459.2 2.608835297 −0.26836909 6.99E−18 0.005865841 0 0.02523 195. ARS2 NM_015908.4 2.602017661 −0.20020565 5.95E−18 0.03056309 0 0.09388 196. YRDC NM_024640.3 2.600956126 0.000579047 1.56E−18 0.994305939 0 0.99763 197. USP29 NM_020903.2 2.596878397 −0.09045716 3.88E−18 0.293726512 0 0.48842 198. EYA3 NM_001990.2 2.572156831 −0.016718 8.10E−18 0.848369803 0 0.91967 199. LOC646914 XM_929877.1 2.569191334 −0.02473384 9.21E−18 0.778586131 0 0.87953 200. PABPN1 NM_004643.1 2.567302816 −0.25853738 3.01E−18 0.005006723 0 0.02213 201. MGC40489 XR_016048.1 2.541736559 −0.46037932 1.56E−16 0.000170117 0 0.00129 202. Cllorf82 NM_145018.2 2.530678429 −0.27379577 2.31E−17 0.006360255 0 0.02696 203. C14orf102 NM_017970.2 2.529377841 0.176891759 4.39E−18 0.044016052 0 0.12468 204. FAM107B NM_031453.2 2.529113421 −0.18414043 7.44E−17 0.067746068 0 0.17309 205. CYCSL1 NR_001561.1 2.505598739 0.37325739 2.32E−18 0.000131642 0 0.00104 206. DEFB103B NM_018661.3 2.499063846 −0.03506737 1.60E−15 0.754511987 0 0.86535 207. LOC646508 XM_937570.1 2.498284454 −0.04201402 4.66E−17 0.652242402 0 0.79692 208. CSRNP3 NM_024969.2 2.495907791 −0.07940541 2.30E−16 0.435421955 0 0.62628 209. CXADR NM_001338.3 2.494457445 −0.07004782 6.78E−16 0.514379205 0 0.69223 210. C13orf34 NM_024808.2 2.49194451 −0.00212698 3.53E−18 0.979075125 0 0.99072 211. LOC100134322 XR_037416.1 2.488088458 0.19623414 1.37E−17 0.033397294 0 0.10071 212. PRAMEF21 NM_001100114.1 2.487018924 −0.06826812 3.03E−17 0.454028195 0 0.64319 213. LOC728450 XM_001131473.2 2.474009279 0.134655982 1.20E−17 0.127894561 0 0.27504 214. SFRS17A NM_005088.2 2.456301079 0.240381708 3.93E−17 0.014336264 0 0.05183 215. FLJ45139 NM_001001692.1 2.451388314 0.100850114 8.41E−16 0.347811335 0 0.54453 216. C6orf117 NM_138409.1 2.446043441 −0.06998426 1.53E−17 0.419253401 0 0.61133 217. NOLC1 NM_004741.1 2.438536354 0.49765378 1.73E−17 1.09E−05 0 0.00013 218. SYNJ1 NM_203446.1 2.433164214 −0.07514634 2.72E−16 0.452617734 0 0.64184 219. MGC10997 NR_001565.1 2.426009364 −0.29360506 2.86E−18 0.001131964 0 0.00638 220. LOC649563 XM_938635.2 2.424763127 −0.0611379 1.45E−16 0.525444143 0 0.70146 221. KPNA2 NM_002266.2 2.416323657 −0.50749956 2.90E−16 4.68E−05 0 0.00044 222. MIR2278 NR_031755.1 2.412240829 0.097675867 2.53E−15 0.382579115 0 0.57813 223. ZNF622 NM_033414.2 2.40621318 0.014027344 6.58E−18 0.862356543 0 0.92843 224. CTR9 NM_014633.3 2.402374134 −0.02160461 1.54E−17 0.798169527 0 0.89173 225. NCRNA00092 NR_024129.1 2.394551708 −0.11225744 3.98E−16 0.267969634 0 0.45928 226. FAM46C NM_017709.3 2.389165515 −0.12894575 5.82E−14 0.325974529 0 0.52277 227. SLC2A14 NM_153449.2 2.374348717 0.247150911 5.24E−16 0.021643048 0 0.07182 228. PRRG4 NM_024081.4 2.369418474 0.209621361 8.34E−16 0.051930043 0 0.14159 229. SLIT2 NM_004787.1 2.368717174 0.850098551 2.92E−17 3.76E−09 0 0 230. CRY1 NM_004075.2 2.341679414 −0.12675954 1.85E−17 0.13815092 0 0.28994 231. ID2 NM_002166.4 2.335808841 0.275613793 3.13E−15 0.018296862 0 0.06306 232. PRAMEF19 NM_001099790.1 2.335767802 −0.03732366 5.68E−18 0.632899653 0 0.78322 233. NFYA NM_002505.3 2.334723566 0.915312276 4.47E−16 9.21E−09 0 0 234. LOC732416 XM_001133386.1 2.328833136 0.05578418 4.22E−17 0.519939778 0 0.69684 235. NUP50 NM_007172.3 2.323544688 1.034765786 1.70E−17 5.78E−11 0 0 236. LOC645137 XM_928167.2 2.322677192 −0.15240225 7.82E−17 0.097906179 0 0.22652 237. LOC651709 XM_001732813.1 2.304254222 0.094448257 2.01E−17 0.257839464 0 0.44705 238. TMEM185A NM_032508.1 2.292123236 0.232711608 2.08E−17 0.009348785 0 0.03688 239. LOC648533 XM_937587.1 2.283913086 0.037364122 5.74E−13 0.790074552 0 0.88629 240. WDR47 NM_014969.4 2.276954944 0.140077923 4.04E−16 0.150823161 0 0.30902 241. RMRP NR_003051.2 2.266910293 0.073341561 1.81E−15 0.476105118 0 0.66141 242. C8orf33 NM_023080.1 2.250696465 −0.06074557 5.76E−17 0.476217777 0 0.66141 243. DUSP12 NM_007240.1 2.249346009 0.098691596 6.04E−18 0.199416906 0 0.37517 244. FAM90A9 XM_496956.4 2.247726801 0.016928845 1.30E−16 0.847999834 0 0.91942 245. ARIH1 NM_005744.2 2.24300359 0.783967696 3.40E−17 6.64E−09 0 0 246. TRIM23 NM_001656.3 2.234876163 0.630256517 7.41E−18 5.77E−08 0 0 247. ADPGK NM_031284.3 2.232580766 0.091955001 2.16E−17 0.257304543 0 0.44637 248. PVRL3 NM_015480.1 2.223358786 0.447298551 1.67E−15 0.000209677 0 0.00154 249. ZNF214 NM_013249.1 2.219239817 0.16599169 2.09E−14 0.156088036 0 0.31667 250. HSPH1 NM_006644.2 2.216889189 −0.48791765 1.07E−17 2.89E−06 0 4.00E−05 251. PIM1 NM_002648.2 2.214932099 −0.67564311 4.69E−18 1.13E−08 0 0 252. PSPN NM_004158.2 2.202671331 −0.0387554 1.84E−15 0.697279542 0 0.82706 253. HOXB2 NM_002145.3 2.202149933 −0.04068855 9.93E−17 0.634244204 0 0.7842 254. LOC100133588 XM_001714755.1 2.200369303 0.039776542 5.95E−14 0.739658675 0 0.85497 255. C1orf63 NM_020317.3 2.189819772 −0.13903881 2.44E−12 0.344977916 0 0.54172 256. STK3 NM_006281.2 2.185603351 −0.21498857 3.10E−15 0.044513409 0 0.12581 257. HEY1 NM_001040708.1 2.180101337 −0.04270689 1.45E−16 0.621081524 0 0.77541 258. LOC728429 XR_038921.1 2.177569373 −0.02833864 2.42E−15 0.776523643 0 0.87813 259. HNRPDL NR_003249.1 2.175352802 0.016888999 1.34E−16 0.843620455 0 0.91755 260. LOC727846 XM_001126140.1 2.175344255 0.003661846 2.12E−15 0.970479736 0 0.98654 261. LOC391045 XM_372780.3 2.165905106 0.353079083 2.62E−14 0.004826112 0 0.02149 262. UBL3 NM_007106.2 2.164486474 −0.80700031 8.07E−17 4.82E−09 0 0 263. ZSCAN2 NM_017894.4 2.151267294 −0.19990085 8.39E−17 0.023707117 0 0.07732 264. PNO1 NM_020143.2 2.150848548 0.248468101 2.17E−17 0.003888212 0 0.018 265. GPR37 NM_005302.2 2.121339069 0.215068748 1.36E−14 0.054464486 0 0.14697 266. TSPAN13 NM_014399.3 2.116834376 −0.14687037 1.64E−15 0.133289273 0 0.28287 267. SNIP1 NM_024700.2 2.104097443 −0.17404984 4.31E−17 0.03536112 0 0.10521 268. MED26 NM_004831.3 2.099784167 0.137079716 5.67E−16 0.135137322 0 0.28545 269. C6orf191 NM_001010876.1 2.090649638 −0.05752287 1.93E−15 0.545204643 0 0.71727 270. LOC645381 XR_038557.1 2.089101452 −0.1265825 1.39E−16 0.135422085 0 0.28587 271. PPP1R15A NM_014330.2 2.079608755 0.566757113 1.80E−16 1.15E−06 0 2.00E−05 272. RRN3 NM_018427.3 2.068096238 0.107184797 2.56E−16 0.212066606 0 0.39151 273. CBARA1 NM_006077.2 2.064175867 −0.15426321 2.91E−15 0.117698621 0 0.25949 274. NGDN NM_015514.1 2.057504656 0.408772415 1.43E−15 0.000219075 0 0.0016 275. MED31 NM_016060.2 2.054924581 0.31225842 3.76E−16 0.001432204 0 0.00778 276. SON NM_032195.1 2.054844468 −0.28384608 5.39E−15 0.008436028 0 0.03398 277. STX6 NM_005819.4 2.053005326 −0.46956758 5.95E−15 0.00010875 0 0.00088 278. C1orf55 NM_152608.3 2.049481602 −0.36315178 8.73E−15 0.001592623 0 0.00851 279. SGK NM_005627.2 2.039844812 −0.11041486 4.65E−16 0.206764605 0 0.38453 280. RPPH1 NR_002312.1 2.037174446 0.226914242 2.02E−15 0.022037966 0 0.07279 281. CEP78 NM_032171.1 2.035493751 −0.13956271 1.64E−16 0.096278858 0 0.22372 282. CASP6 NM_032992.2 2.035084058 0.233567145 3.68E−15 0.02223849 0 0.07334 283. ARID3B NM_006465.2 2.024103942 −0.0745492 2.94E−16 0.373855818 0 0.56922 284. AVPI1 NM_021732.1 2.021560017 0.188378801 9.68E−17 0.024283729 0 0.07885 285. RNGTT NM_003800.3 2.017732238 −0.59159318 4.94E−17 1.45E−07 0 0 286. KIAA0020 NM_014878.4 2.017163694 0.017829862 1.80E−15 0.844688542 0 0.91796 287. SLC25A44 NM_014655.1 2.016768709 −0.0765425 1.49E−16 0.343019748 0 0.5399 288. RBM12 NM_006047.4 2.012922532 −0.37476245 1.03E−16 9.94E−05 0 0.00082 289. CXCR4 NM_001008540.1 2.003654471 −0.05210245 2.10E−14 0.613887002 0 0.76996 290. PDSS1 NM_014317.3 2.002705196 −0.07459033 1.33E−15 0.405603148 0 0.59918 291. ISOC1 NM_016048.1 2.002585299 −0.61873447 7.89E−16 5.78E−07 0 1.00E−05 292. SERTAD1 NM_013376.3 2.001534685 0.410030021 1.32E−14 0.000524692 0 0.00336 293. CCDC58 NM_001017928.2 2.001365764 0.076783734 3.92E−15 0.418170823 0 0.6105 294. DNAJC25 NM_001015882.2 1.995453072 −0.50719957 5.50E−17 1.28E−06 0 2.00E−05 295. LSG1 NM_018385.1 1.994244729 −0.06468359 7.42E−16 0.454331188 0 0.64342 296. HSPA6 NM_002155.3 1.993905834 0.128022925 1.90E−16 0.120483692 0 0.26369 297. FRG2B NM_001080998.1 1.993396796 0.13147002 1.21E−15 0.146280541 0 0.30263 298. CD9 NM_001769.2 1.991567881 −0.00478773 2.64E−14 0.96313223 0 0.98338 299. LOC652080 XM_941404.1 1.987117494 0.173413351 8.20E−15 0.085827376 0 0.20642 300. RAB11FIP1 NM_001002814.1 1.98677521 −0.47650768 2.06E−16 7.22E−06 0 9.00E−05 301. RBBP6 NM_032626.5 1.98571063 −0.1339181 2.18E−13 0.255048947 0 0.4434 302. INO80C NM_194281.3 1.979828473 −0.11275614 3.37E−14 0.286888863 0 0.48127 303. TRA2A NM_013293.3 1.977977513 −0.10947385 1.54E−15 0.224834701 0 0.40702 304. LYAR NM_017816.1 1.97693312 0.000874971 1.25E−15 0.992016109 0 0.99687 305. C1QTNF3 NM_181435.4 1.974262994 −0.02264422 1.81E−16 0.774302617 0 0.87667 306. KLC1 NM_005552.4 1.96683651 −0.06609191 1.44E−15 0.454063934 0 0.6432 307. LOC399988 XR_018287.2 1.965863889 −0.41310115 2.86E−15 0.000178798 0 0.00134 308. MED10 NM_032286.2 1.965185968 0.599425454 1.80E−16 2.22E−07 0 1.00E−05 309. LOC391763 XM_001715080.1 1.963119789 0.092872676 3.74E−13 0.434006893 0 0.62476 310. RGS4 NM_005613.3 1.951453189 −0.48369978 1.18E−15 1.53E−05 0 0.00017 311. POLR3K NM_016310.2 1.950192615 0.058729235 5.12E−15 0.529572686 0 0.7048 312. OSBPL8 NM_020841.4 1.950078352 1.0547593 5.57E−15 3.91E−10 0 0 313. PNN NM_002687.3 1.949442084 0.044126108 3.43E−16 0.585331055 0 0.74731 314. TUBB2C NM_006088.5 1.948000242 −0.53914845 2.08E−16 1.03E−06 0 2.00E−05 315. SNAI1 NM_005985.2 1.943131852 −0.03657258 1.02E−14 0.703998321 0 0.83171 316. LOC651390 XM_942401.1 1.937495897 −0.07745626 2.67E−14 0.445805611 0 0.63538 317. EXOSC10 NM_002685.2 1.936970335 0.277137164 1.08E−11 0.058545399 0 0.15506 318. GPBAR1 NM_170699.2 1.936378949 −0.12982997 7.31E−15 0.177666352 0 0.34619 319. NEFH NM_021076.2 1.936165554 0.099517054 9.82E−15 0.304158408 0 0.49929 320. PEG10 XM_499343.2 1.93541239 −0.09718045 4.86E−13 0.413319297 0 0.60668 321. LOC643336 XM_001718563.1 1.933728249 1.023196188 1.62E−15 1.85E−10 0 0 322. HNRPA1L-2 NR_002944.2 1.921260156 −0.89796096 5.13E−16 5.51E−10 0 0 323. FRAT2 NM_012083.2 1.918313267 −0.05118051 5.04E−16 0.529046462 0 0.70431 324. HSPB3 NM_006308.1 1.913506168 −0.79338174 3.48E−14 1.44E−07 0 0 325. CRLF3 NM_015986.2 1.911700836 −0.14486974 2.52E−16 0.073921065 0 0.18466 326. MIR503 NR_030228.1 1.909586785 −0.13610263 6.88E−14 0.202499117 0 0.37906 327. POLR1B NM_019014.3 1.90405424 −0.13127473 2.09E−15 0.140374918 0 0.29338 328. LOC643731 XM_927019.1 1.903360811 −0.00093141 4.70E−13 0.993571402 0 0.99732 329. CCDC59 NM_014167.2 1.892481485 0.2508832 4.34E−15 0.010195171 0 0.03944 330. ETNK1 NM_001039481.1 1.89168344 0.064440994 3.57E−13 0.570766866 0 0.73739 331. NOP58 NM_015934.3 1.886662902 0.224260185 1.13E−15 0.012880266 0 0.04768 332. BRIX1 NM_018321.3 1.886222351 0.299106046 7.02E−15 0.003529392 0 0.01657 333. SNRNP70 NM_003089.4 1.884727124 0.017757319 1.78E−15 0.834507764 0 0.91261 334. ELOF1 NM_032377.3 1.884130525 −0.30080573 3.39E−15 0.002480132 0 0.0123 335. CCNT2 NM_058241.1 1.876469209 −0.32206863 7.60E−16 0.0006697 0 0.00412 336. NANS NM_018946.2 1.871711876 −0.00660686 4.71E−14 0.947536181 0 0.97449 337. LOC100129630 XM_001714940.1 1.870936058 −0.10375837 1.63E−14 0.281144687 0 0.47443 338. TAF4B NM_005640.1 1.86960695 −0.04440194 6.38E−14 0.663918819 0 0.805 339. SRP19 NM_003135.1 1.866226706 0.227022607 8.39E−15 0.020599821 0 0.06904 340. SGCG NM_000231.1 1.863213339 0.125027437 3.80E−15 0.163210943 0 0.32631 341. CCNE1 NM_057182.1 1.863055664 −0.12768816 3.24E−13 0.257494264 0 0.44663 342. SLC40A1 NM_014585.3 1.858510401 −0.42386003 3.33E−15 7.95E−05 0 0.00068 343. PKIB NM_032471.4 1.858446651 −0.17186416 2.73E−14 0.087611639 0 0.20959 344. LARP1B NM_032239.2 1.857923432 −0.26022457 3.16E−16 0.002599598 0 0.01279 345. SNORD56 NR_002739.1 1.854937162 −0.16574948 6.20E−14 0.112311042 0 0.25059 346. SIRT1 NM_012238.3 1.843963503 0.207080634 2.73E−13 0.068322693 0 0.1741 347. KIAA0114 NR_024031.1 1.840881565 −0.31600952 3.86E−14 0.003849075 0 0.01784 348. LOC399937 XM_374917.3 1.840861475 0.000791404 5.08E−14 0.993631669 0 0.99732 349. CLK1 NM_001024646.1 1.840475237 0.075199503 3.48E−12 0.548449186 0 0.71998 350. LOC391092 XM_372792.2 1.837421253 0.110663076 9.40E−14 0.286465176 0 0.48071 351. SEC61A2 NM_018144.2 1.837165462 0.209041091 3.40E−15 0.022761839 0 0.07478 352. KIF21A NM_017641.2 1.836729176 0.015294409 2.76E−15 0.856782313 0 0.92516 353. LOC651816 XM_941060.1 1.836368433 −0.53879136 3.60E−15 3.67E−06 0 5.00E−05 354. KCNA1 NM_000217.2 1.831756083 0.028418893 6.64E−13 0.802216761 0 0.89368 355. PPM1B NM_177968.2 1.830564265 −0.03419808 1.49E−14 0.71162437 0 0.83624 356. MYLIP NM_013262.3 1.824056957 −0.29688235 2.69E−15 0.001923181 0 0.00997 357. KATNA1 NM_007044.2 1.819203659 0.113184818 6.97E−15 0.208410535 0 0.3867 358. MBD2 NM_015832.3 1.817924533 −0.07679197 5.80E−15 0.383295862 0 0.5789 359. MED13 NM_005121.2 1.816759236 0.026398068 1.83E−15 0.747828875 0 0.86101 360. SOX4 NM_003107.2 1.808997932 −0.21735552 7.84E−14 0.039377791 0 0.11469 361. SERPINI1 NM_005025.3 1.808914219 0.035398211 1.10E−14 0.694040672 0 0.82487 362. LOC389633 XM_372030.4 1.806620634 −0.08520179 1.06E−14 0.346747877 0 0.54351 363. CHORDC1 NM_012124.1 1.804721727 0.126125821 3.39E−15 0.144922027 0 0.30054 364. ARC NM_015193.3 1.801587557 −0.18800477 2.20E−15 0.031295976 0 0.09574 365. INSM1 NM_002196.2 1.800557044 0.230573913 1.78E−14 0.019367652 0 0.06592 366. RBM39 NM_184234.1 1.799763318 0.263046794 2.84E−14 0.010347921 0 0.0399 367. LOC642538 XM_926027.2 1.792389919 0.125787579 2.61E−14 0.186933675 0 0.35927 368. TESK2 NM_007170.2 1.787330928 0.126864846 4.92E−15 0.146548958 0 0.30296 369. PDRG1 NM_030815.2 1.782963685 0.062203847 4.00E−14 0.514127 0 0.69201 370. KLF17 NM_173484.3 1.778806102 0.080447536 4.47E−14 0.402160621 0 0.59562 371. FAM90A12 XM_496961.3 1.774389657 0.048242903 9.46E−14 0.626471745 0 0.77881 372. LOC388275 XM_928429.1 1.772108431 −0.93959193 1.86E−14 1.63E−09 0 0 373. ZNF365 NM_014951.2 1.771160957 −0.37403373 2.58E−14 0.000552145 0 0.00351 374. RNF122 NM_024787.2 1.768869814 0.191599957 3.76E−14 0.051887596 0 0.14151 375. KDM5B NM_006618.3 1.762560409 −0.11116732 1.38E−14 0.218359857 0 0.39927 376. HOXB6 NM_018952.4 1.761678941 0.064514742 6.42E−14 0.504431835 0 0.68485 377. C21orf91 NM_017447.2 1.759665752 0.079481476 5.99E−14 0.409986098 0 0.60376 378. FAM90A5 XM_496947.4 1.757517326 0.104189301 1.59E−15 0.19548293 0 0.37021 379. FAM133B NM_152789.2 1.756086039 0.088582621 2.09E−14 0.331959546 0 0.52857 380. NIPSNAP3A NM_015469.1 1.750667829 −0.06938901 1.89E−14 0.441356857 0 0.63143 381. RNF152 NM_173557.2 1.749157783 0.225296538 1.87E−13 0.035514631 0 0.10551 382. C13orf31 NM_153218.1 1.748039669 0.014786819 1.38E−14 0.866326588 0 0.93043 383. ELOVL4 NM_022726.2 1.746070975 −0.32373904 2.27E−15 0.000556816 0 0.00353 384. TP53BP2 NM_001031685.2 1.746064864 −0.03883125 9.55E−15 0.652528964 0 0.79705 385. RGMB NM_173670.2 1.744692748 −0.08083442 3.88E−14 0.387433275 0 0.58277 386. SNORD57 NR_002738.1 1.743583957 −0.13727561 3.02E−14 0.143871452 0 0.29888 387. B3GNT2 NM_006577.5 1.7399837 0.250805704 1.11E−14 0.008204737 0 0.03325 388. RHPN2 NM_033103.3 1.737884672 0.158675469 2.56E−15 0.058054713 0 0.15405 389. YARS2 NM_001040436.1 1.734675756 0.142331612 1.56E−14 0.116254974 0 0.25685 390. SHISA2 NM_001007538.1 1.730687009 −0.29083242 2.65E−14 0.003885633 0 0.01799 391. IRX5 NM_005853.5 1.727349949 0.188078458 3.74E−14 0.050714653 0 0.13905 392. ALG13 NM_018466.3 1.725153512 0.27014979 1.71E−14 0.005461924 0 0.02376 393. STAU1 NM_017453.2 1.725139964 0.220644256 1.02E−14 0.016547772 0 0.05821 394. EAF1 NM_033083.6 1.723531505 0.009204673 1.84E−13 0.926295141 0 0.96428 395. LOC440258 NM_001013702.1 1.72092305 0.222949425 4.34E−14 0.023466916 0 0.07668 396. HNRPA1P4 XM_939887.2 1.720333337 −1.13055551 7.21E−15 1.63E−11 0 0 397. LOC730081 XR_041261.1 1.720102785 0.285804464 5.43E−14 0.005563248 0 0.02411 398. CDKN2AIP NM_017632.2 1.718073072 0.331152557 5.13E−14 0.001738143 0 0.00916 399. LOC440061 XR_037839.1 1.712654514 −0.25460059 3.16E−12 0.037315128 0 0.10986 400. C16orf80 NM_013242.2 1.710982277 −0.18355681 2.36E−14 0.048676471 0 0.13456 401. CTH NM_153742.3 1.708483062 0.2684476 1.19E−14 0.004647673 0 0.02082 402. DDX47 NM_016355.3 1.708313699 0.248170569 1.77E−15 0.003940592 0 0.01819 403. TFB2M NM_022366.1 1.708281567 −0.01288396 2.95E−14 0.88539985 0 0.94104 404. C1orf52 NM_198077.2 1.703202814 −0.22109401 9.07E−16 0.006815725 0 0.02859 405. C14orf138 NM_001040662.1 1.702642937 0.300283903 1.34E−14 0.001999261 0 0.0103 406. AURKAPS1 NR_001587.1 1.70161228 0.068219051 2.34E−15 0.385267608 0 0.58075 407. ARPP-21 NM_001025068.1 1.69906582 0.013710129 3.79E−13 0.893086928 0 0.94527 408. PRPF18 NM_003675.3 1.698120259 0.343027256 2.69E−13 0.002458302 0 0.01222 409. WDR43 XM_944889.1 1.688207463 0.98248568 2.28E−14 4.03E−10 0 0 410. SLC25A4 NM_001151.2 1.68799987 0.228376088 2.32E−13 0.029717308 0 0.09193 411. EIF4A3 NM_014740.2 1.682073483 −0.02293191 7.82E−15 0.779929294 0 0.88037 412. SNORD68 NR_002450.1 1.678911456 0.096404262 8.09E−15 0.247869843 0 0.43546 413. LOC729423 XM_001726952.1 1.67695359 −0.81244327 4.52E−12 7.23E−07 0 1.00E−05 414. MAP2 NM_002374.3 1.676115893 1.955494491 3.97E−13 2.26E−14 0 0 415. TUBB4Q NM_020040.3 1.675304726 −0.29288776 1.74E−13 0.006038937 0 0.02585 416. MAD2L1BP NM_014628.2 1.674485119 0.49354184 1.75E−14 1.05E−05 0 0.00013 417. NUP98 NM_016320.3 1.674194958 −0.17098799 5.36E−15 0.042873219 0 0.12239 418. TDG NM_003211.3 1.674073464 0.174499498 1.04E−13 0.074107463 0 0.18496 419. TCEB3 NM_003198.1 1.673830159 0.528724598 4.16E−15 1.48E−06 0 2.00E−05 420. PTP4A1 NM_003463.3 1.672611158 −0.12680128 2.38E−14 0.153505006 0 0.31292 421. HSPA8 NM_153201.1 1.666088959 −0.34827432 1.87E−14 0.00051701 0 0.00332 422. UBL5 NM_024292.2 1.665307847 −0.10865722 2.41E−13 0.272792946 0 0.4649 423. C2orf56 NM_001083946.1 1.661422458 0.281261857 2.36E−14 0.003507891 0 0.01649 424. MAST4 NM_198828.2 1.658879828 0.031824635 1.15E−14 0.700387125 0 0.82933 425. BCL2L12 NM_001040668.1 1.656287859 −0.3354186 1.93E−14 0.000708935 0 0.00432 426. INVS NM_183245.1 1.652697508 0.431685941 1.42E−13 0.00016241 0 0.00124 427. CDC42 NM_001039802.1 1.650469411 0.562942841 4.05E−14 2.74E−06 0 4.00E−05 428. ATF3 NM_001040619.1 1.647975758 1.164189073 1.21E−13 6.55E−11 0 0 429. HEY2 NM_012259.1 1.643903866 0.097146095 7.56E−13 0.348571796 0 0.54507 430. ZSWIM6 XM_035299.8 1.642128642 −0.4778082 1.46E−14 1.09E−05 0 0.00013 431. C3orf58 NM_173552.2 1.641296279 0.01647501 1.46E−12 0.87657807 0 0.93618 432. LOC401097 XM_941354.2 1.638403413 −0.11820885 2.04E−13 0.222817497 0 0.40457 433. EGLN1 NM_022051.1 1.637555803 1.211267396 7.84E−14 1.92E−11 0 0 434. CUGBP1 NM_001025596.1 1.6340811 0.303511987 3.48E−14 0.001989256 0 0.01026 435. LOC642678 XM_926130.1 1.63220557 0.263521524 9.61E−15 0.003494982 0 0.01644 436. C15orf60 NM_001042367.1 1.630853946 −0.02529098 4.33E−15 0.743037038 0 0.85707 437. PHAX NM_032177.2 1.630648972 0.499748672 1.47E−14 5.57E−06 0 7.00E−05 438. MED6 NM_005466.2 1.62829406 0.234613809 7.47E−15 0.007155742 0 0.02974 439. CTNNAL1 NM_003798.2 1.625720574 −0.17578358 3.23E−14 0.050525454 0 0.13863 440. PDK3 NM_005391.2 1.625329362 0.772620864 4.98E−14 2.32E−08 0 0 441. PLEKHB2 NM_001031706.1 1.622273401 0.054655486 3.21E−14 0.523709551 0 0.70026 442. NUDT11 NM_018159.3 1.621197373 −0.57819231 2.56E−15 1.73E−07 0 0 443. BDNF NM_170732.3 1.620223761 0.035311781 1.84E−11 0.769673882 0 0.8738 444. NGLY1 NM_018297.2 1.61360189 0.298383033 2.22E−15 0.000564863 0 0.00357 445. ZNF705D NM_001039615.3 1.610202541 −0.02597342 5.30E−13 0.792068462 0 0.88765 446. MED15 NM_001003891.1 1.609997025 −0.06790583 9.68E−14 0.452731449 0 0.64195 447. ZIK1 NM_001010879.2 1.609559281 0.460511424 6.70E−14 3.67E−05 0 0.00036 448. PRPF40A NM_017892.3 1.60701676 0.43524072 1.48E−14 2.68E−05 0 0.00027 449. PMAIP1 NM_021127.1 1.605658964 0.635854476 1.01E−10 9.09E−05 0 0.00076 450. KRTAP2-1 XM_926554.2 1.605615798 −0.00836408 2.52E−12 0.937638775 0 0.96996 451. SNORA67 NR_002912.1 1.603876448 −0.01990015 4.24E−13 0.837308572 0 0.9142 452. NKIRAS1 NM_020345.3 1.602380221 −0.21505265 7.40E−15 0.011263604 0 0.04272 453. SAMD8 NM_144660.1 1.599343462 0.673947538 1.53E−12 2.24E−06 0 3.00E−05 454. LOC728408 XR_039142.1 1.597556992 0.195973187 1.22E−13 0.039933909 0 0.11598 455. MAPKAP1 NM_001006618.1 1.596744892 0.290086205 3.92E−15 0.000881923 0 0.0052 456. ECD NM_007265.1 1.596500869 0.440442679 6.46E−13 0.000216775 0 0.00159 457. TOPORS NM_005802.2 1.595626451 0.418698719 3.87E−15 1.65E−05 0 0.00018 458. RTN4 NM_007008.2 1.593944683 0.264653804 4.43E−13 0.011750635 0 0.04419 459. ARHGAP19 NM_032900.4 1.593323373 −0.26239597 8.31E−14 0.006924484 0 0.02897 460. SH3GL2 NM_003026.1 1.59238137 0.073484379 2.15E−13 0.431704365 0 0.62263 461. MYBPH NM_004997.2 1.591566604 −0.44577378 2.98E−11 0.001408545 0 0.00767 462. NT5DC3 NM_016575.1 1.590953067 −0.47059679 2.60E−15 2.60E−06 0 4.00E−05 463. SNRPN NM_022807.2 1.589618988 −0.17582455 1.07E−13 0.059789988 0 0.15751 464. GJA1 NM_000165.3 1.58780493 −0.178685 1.61E−12 0.094898465 0 0.22167 465. LOC400013 XR_039228.1 1.587250344 0.031497834 6.92E−15 0.682627414 0 0.81743 466. HNRNPM NM_031203.2 1.586899323 −0.14982292 1.50E−14 0.072940459 0 0.1828 467. STX3 NM_004177.3 1.581157146 0.356650082 3.87E−13 0.00114871 0 0.00645 468. LOC644914 XM_930111.2 1.575423572 −0.06923633 6.93E−09 0.676335846 0 0.81295 469. LOC100133836 XM_001713608.1 1.575168029 0.10564662 8.84E−13 0.292962838 0 0.48767 470. GTF2B NM_001514.3 1.574967456 0.347163622 1.99E−15 8.61E−05 0 0.00073 471. SCML1 NM_001037540.1 1.574201734 0.188494795 7.40E−13 0.065842365 0 0.16936 472. TBPL1 NM_004865.2 1.573806979 0.205833238 8.90E−14 0.02721547 0 0.08586 473. ZNF551 NM_138347.2 1.568648262 −0.00011162 7.49E−13 0.999088618 0 0.99958 474. SFRS10 NM_004593.1 1.5681537 −0.75201357 4.24E−14 1.76E−08 0 0 475. OXR1 NM_181354.3 1.562540281 −0.71933778 1.96E−14 1.74E−08 0 0 476. BHLHE22 NM_152414.3 1.560252215 0.101626343 2.45E−13 0.274055287 0 0.46656 477. OR6X1 NM_001005188.1 1.558631453 −0.12817436 3.38E−13 0.178290073 0 0.34676 478. LMO4 NM_006769.2 1.557490718 0.353184397 4.70E−14 0.000377316 0 0.00254 479. LOC645166 XM_001129441.2 1.554857161 0.192882939 2.99E−14 0.026452044 0 0.08411 480. STIL NM_003035.2 1.55295308 −0.4828307 5.72E−14 1.19E−05 0 0.00014 481. LOC100133760 XM_001719676.1 1.552936795 0.16059717 1.79E−13 0.084458299 0 0.20408 482. FZD7 NM_003507.1 1.550854894 −0.13090274 2.74E−13 0.16304396 0 0.32612 483. BTAF1 NM_003972.2 1.549813547 0.070013752 6.30E−13 0.467209265 0 0.65411 484. CCNC NM_005190.3 1.54954803 0.095974423 1.98E−14 0.235071298 0 0.41982 485. DNAJB1 NM_006145.1 1.54841722 −0.33172027 3.62E−14 0.000572756 0 0.00361 486. ASB7 NM_024708.2 1.548080129 0.274794966 3.54E−14 0.002879842 0 0.01399 487. DDX39 NM_005804.2 1.547089571 0.1754289 2.56E−13 0.065048264 0 0.16785 488. LOC85389 NR_001453.1 1.546684873 0.007015657 1.79E−12 0.944650057 0 0.97324 489. APIP NM_015957.1 1.542886454 −0.00581131 4.45E−15 0.936540677 0 0.96961 490. ZNF330 NM_014487.3 1.540957622 −0.07386804 2.12E−13 0.413978578 0 0.60714 491. ABL1 NM_007313.2 1.539307052 0.145489802 4.48E−13 0.130010749 0 0.27803 492. WDR45L NM_019613.2 1.538237535 0.360400213 7.47E−14 0.000349259 0 0.00237 493. CDR2 NM_001802.1 1.53742338 −0.30870921 9.68E−14 0.001642031 0 0.00874 494. LOC648040 XM_937090.1 1.53646268 0.053464634 5.12E−13 0.570118838 0 0.73692 495. TMSB15A NM_021992.2 1.535257062 −1.12870839 6.88E−14 1.89E−11 0 0 496. DDX3X NM_001356.3 1.533546299 −0.1679824 1.05E−12 0.096033914 0 0.2235 497. TAF5 NM_006951.3 1.533278341 −0.20722919 1.52E−13 0.026663375 0 0.0846 498. SNORA80 NR_002996.2 1.531309838 0.08504288 4.65E−14 0.306803596 0 0.5021 499. LOC731049 XM_001129232.1 1.530043889 −0.70866978 7.11E−12 1.95E−06 0 3.00E−05 500. RBM14 NM_006328.2 1.527566336 −0.21778628 2.56E−14 0.011666847 0 0.04393 501. CNNM4 NM_020184.3 1.523298011 0.02269985 1.51E−12 0.818049687 0 0.90311 502. GLS NM_014905.2 1.52096024 −0.80631784 2.48E−14 2.12E−09 0 0 503. METTL7B NM_152637.1 1.518189623 −0.55481484 4.95E−13 6.63E−06 0 9.00E−05 504. RSRC2 NM_023012.4 1.514721977 −0.1150749 1.90E−14 0.148027453 0 0.30524 505. FAM90A17 XM_001129363.2 1.513614783 −0.09546518 1.31E−13 0.273354754 0 0.46568 506. SLU7 NM_006425.4 1.512152853 0.717990416 3.02E−14 1.54E−08 0 0 507. LOC654256 XM_942353.1 1.509691066 0.003681464 2.30E−12 0.970637014 0 0.98654 508. LOC730820 XM_001127763.1 1.506653829 0.257075032 7.79E−14 0.005290665 0 0.02314 509. GLMN NM_053274.2 1.506236955 −0.16030238 1.21E−12 0.107692491 0 0.24313 510. LOC728640 XR_015400.1 1.506174187 −0.16289752 1.38E−13 0.068584855 0 0.17462 511. NUP54 NM_017426.2 1.503392773 0.027683096 2.48E−13 0.753930426 0 0.8649 512. AHR NM_001621.3 1.500923505 1.64275074 4.05E−13 7.61E−14 0 0 513. H2AFZ NM_002106.3 1.499572269 −0.3879234 9.97E−13 0.000523412 0 0.00335 514. C1orf128 NM_020362.3 1.497934427 −0.06705701 1.71E−14 0.383082842 0 0.57869 515. RNF4 NM_002938.2 1.497336031 −0.25222173 1.90E−13 0.008011302 0 0.03261 516. TFAP2C NM_003222.3 1.496945403 −0.18736367 5.78E−13 0.052500579 0 0.14285 517. C1orf185 XM_209252.6 1.49683368 0.058034061 3.70E−11 0.617231268 0 0.77232 518. BRD2 NM_005104.2 1.495026143 0.083794647 2.68E−14 0.288647235 0 0.48332 519. RAB3IP NM_175624.2 1.494489505 0.11802541 3.56E−13 0.196543599 0 0.37153 520. PITX1 NM_002653.3 1.494464327 0.245507893 7.06E−13 0.014555822 0 0.05244 521. ALG11 NM_001004127.1 1.493839221 0.493936201 1.03E−12 3.81E−05 0 0.00037 522. TCP1 NM_030752.2 1.493545632 −0.05603384 4.05E−12 0.584510317 0 0.74675 523. DHX9 NM_001357.3 1.493186665 −0.0171031 2.72E−13 0.846033265 0 0.9184 524. NOL11 NM_015462.3 1.489057392 −0.04128462 8.08E−14 0.616750218 0 0.77192 525. TPM3 NM_152263.2 1.48876168 0.579968022 3.03E−13 1.95E−06 0 3.00E−05 526. LOC283116 XM_208043.4 1.487827846 0.118511077 1.06E−12 0.218730077 0 0.39975 527. RYBP NM_012234.4 1.486399459 −0.35369721 2.11E−14 0.000147008 0 0.00114 528. SNORD43 NR_002439.1 1.48537347 0.039488281 2.52E−11 0.725753871 0 0.84571 529. RHOBTB1 NM_198225.1 1.485256007 −0.45165823 2.03E−13 3.61E−05 0 0.00035 530. LOC641802 XM_935872.1 1.485216463 0.376747849 8.91E−14 0.000169723 0 0.00128 531. HTRA4 NM_153692.2 1.484230449 0.215030394 1.08E−13 0.016696826 0 0.05858 532. ZNF263 NM_005741.3 1.481056926 −0.13718839 3.70E−14 0.09197961 0 0.21695 533. LOC645232 XM_928271.1 1.479784917 −0.00044634 2.41E−12 0.996376666 0 0.99841 534. DI03 NM_001362.2 1.477091363 −0.07106955 1.13E−11 0.508479304 0 0.68767 535. SRFBP1 NM_152546.1 1.475739204 0.45287234 7.60E−14 1.70E−05 0 0.00019 536. DNAJA1 NM_001539.2 1.471203017 0.643687358 8.61E−14 1.34E−07 0 0 537. PPFIBP2 NM_003621.1 1.467327061 −0.00235925 8.11E−12 0.981938862 0 0.99193 538. NDEL1 NM_030808.3 1.467127006 −0.02163182 2.46E−14 0.776179739 0 0.87787 539. RRP15 NM_016052.3 1.465748171 0.165874388 2.22E−14 0.038048251 0 0.11152 540. SUPT6H NM_003170.3 1.464959001 0.257955364 1.11E−11 0.022964207 0 0.07531 541. EIF1 NM_005801.3 1.46472025 −0.21791089 7.47E−13 0.025400915 0 0.08167 542. C1orf187 NM_198545.2 1.46296546 −0.02269906 3.13E−13 0.794138153 0 0.88916 543. SLC35F3 NM_173508.2 1.462545631 −0.09338754 3.92E−11 0.414528519 0 0.60764 544. LOC732387 XR_015868.1 1.45974406 −0.16936331 4.12E−12 0.101560033 0 0.23264 545. DPPA3 NM_199286.2 1.457269792 −0.00424754 3.09E−11 0.969625546 0 0.98648 546. BCCIP NM_078468.1 1.454741172 0.108769507 1.55E−13 0.2007215 0 0.3768 547. FBXW7 NM_033632.2 1.454071129 0.143817093 1.36E−12 0.135509671 0 0.2859 548. LOC732360 XR_038607.1 1.450256538 0.156874564 3.06E−13 0.079962819 0 0.19619 549. ILF2 NM_004515.2 1.450144347 −0.2235945 6.27E−14 0.009657131 0 0.03776 550. TAF7 NM_005642.2 1.44931134 0.260318224 2.95E−12 0.013665045 0 0.05007 551. FBXO28 NM_015176.1 1.449224666 0.332557144 8.84E−14 0.000468708 0 0.00306 552. LOC648390 XR_037845.1 1.446477421 −0.16743094 9.36E−14 0.048260154 0 0.13375 553. LOC100134083 XM_001714551.1 1.444757278 0.065916236 7.44E−11 0.572248293 0 0.73805 554. CDS1 NM_001263.2 1.443156315 −0.03729718 1.11E−10 0.753883222 0 0.8649 555. TMPO NM_003276.1 1.440849718 −0.16059408 6.25E−12 0.122797864 0 0.26716 556. SLC10A4 NM_152679.2 1.438316891 0.131702245 1.31E−12 0.164547852 0 0.32843 557. SFRS2 NM_003016.3 1.43818754 −0.55216219 5.75E−14 6.74E−07 0 1.00E−05 558. LOC100129267 XR_037397.1 1.436698179 −0.10192887 9.54E−13 0.268686055 0 0.46016 559. CSRP2 NM_001321.1 1.436294732 −0.82970582 1.34E−12 1.78E−08 0 0 560. HNRNPA2B1 NM_031243.2 1.436197608 0.130215149 4.15E−13 0.143912138 0 0.29891 561. CLP1 NM_006831.1 1.433554015 0.348572252 2.57E−13 0.000467471 0 0.00305 562. MTF2 NM_007358.2 1.430806129 0.244039964 5.37E−13 0.010617995 0 0.04071 563. C13orf27 NM_138779.2 1.428664756 0.047576445 1.17E−11 0.646885227 0 0.79308 564. MEX3C NM_016626.3 1.427435993 0.093724078 4.05E−13 0.283008406 0 0.47662 565. CBX4 NM_003655.2 1.426881488 0.311472696 2.28E−13 0.001191417 0 0.00666 566. DDX21 NM_004728.2 1.426501707 −0.17094795 1.18E−13 0.043877499 0 0.12445 567. SFRS15 NM_020706.1 1.424894099 0.168074451 2.26E−13 0.054322289 0 0.14667 568. AHCTF1 NM_015446.3 1.422776124 0.285495925 5.55E−14 0.001279213 0 0.00706 569. STARD7 NM_020151.3 1.422197808 0.009352233 7.93E−12 0.926146793 0 0.96426 570. LOC347376 XM_937928.1 1.421140581 −0.31817931 2.93E−09 0.034321047 0 0.10284 571. C6orf66 NM_014165.1 1.417175337 0.119941892 4.37E−13 0.172177225 0 0.33865 572. LOC644330 XR_017492.1 1.414996029 0.663508029 1.07E−10 1.26E−05 0 0.00015 573. ABCG1 NM_207629.1 1.411683724 −0.03110394 1.60E−11 0.765467774 0 0.87176 574. NOV NM_002514.2 1.410494135 −0.04872585 1.01E−11 0.631961219 0 0.7829 575. GFM1 NM_024996.5 1.407835107 −0.79555703 2.13E−13 4.99E−09 0 0 576. LOC652595 XM_942117.1 1.405139131 −0.09810807 1.65E−12 0.290150795 0 0.48482 577. ZNF281 NM_012482.3 1.404648603 −0.00361308 7.00E−13 0.966941631 0 0.98526 578. ARID4B NM_016374.5 1.404306999 0.569331433 8.04E−12 1.25E−05 0 0.00015 579. LOC645233 NR_024382.1 1.403953598 0.103826446 1.83E−12 0.266012715 0 0.45717 580. MYOG NM_002479.4 1.400086822 −0.85712385 5.19E−10 1.19E−06 0 2.00E−05 581. OSR2 XM_001126824.1 1.399885028 0.140060681 4.11E−13 0.108689759 0 0.24479 582. LOC727758 XM_001125808.2 1.396320204 0.343226006 2.86E−12 0.001407708 0 0.00766 583. HIC2 NM_015094.2 1.395105507 −0.07986711 7.32E−14 0.303989988 0 0.49905 584. PHLPP2 NM_015020.2 1.393342712 0.011230089 1.82E−13 0.888929658 0 0.94301 585. LOC728153 XM_001128002.1 1.392470561 −0.1239819 2.15E−12 0.187228802 0 0.35968 586. PHLPP1 NM_194449.1 1.391942682 −0.11204861 1.71E−13 0.171819649 0 0.33813 587. SBNO1 NM_018183.2 1.391640047 0.912611144 3.73E−11 4.46E−08 0 0 588. ZNF574 NM_022752.5 1.391080303 −0.02575443 9.43E−13 0.769404142 0 0.87366 589. BAGE5 NM_182484.1 1.390112085 0.312869895 1.32E−12 0.002062769 0 0.01058 590. EML4 NM_019063.2 1.388253958 −0.89138642 1.80E−12 4.14E−09 0 0 591. SHFM1 NM_006304.1 1.387446578 −0.02974983 3.90E−12 0.753525894 0 0.86487 592. SLC12A2 NM_001046.2 1.386367245 −0.75596 1.01E−11 2.46E−07 0 1.00E−05 593. RND3 NM_005168.3 1.386186726 0.925453193 4.07E−12 4.56E−09 0 0 594. MGAT4C NM_013244.2 1.385868579 −0.0799553 2.07E−12 0.385732105 0 0.58121 595. ERN1 NM_152461.2 1.385516021 −0.07639676 1.49E−12 0.398333442 0 0.59217 596. C16orf87 NM_001001436.2 1.384283092 −0.05230872 1.30E−12 0.557876212 0 0.72752 597. MBIP NM_016586.1 1.383473795 0.279754309 3.55E−13 0.002746197 0 0.0134 598. SUV420H1 NM_016028.4 1.383227676 0.315044495 2.43E−12 0.00245823 0 0.01222 599. MFSD4 NM_181644.2 1.383119443 −0.12045834 4.50E−12 0.214393959 0 0.39439 600. TSC22D2 NM_014779.2 1.382388949 −0.27410124 5.22E−11 0.019370365 0 0.06592 601. FNBP1L NM_001024948.1 1.382235187 −0.88872668 1.36E−12 3.13E−09 0 0 602. SLC25A13 NM_014251.1 1.382003256 −0.09193427 1.14E−12 0.30332903 0 0.49844 603. GAB2 NM_080491.1 1.381903767 −0.22970672 5.75E−13 0.012715227 0 0.04719 604. BMP2K NM_017593.3 1.380005052 0.155131234 3.90E−12 0.110918545 0 0.24845 605. CCK NM_000729.3 1.377654752 −0.04697335 9.98E−14 0.543484917 0 0.71617 606. GCC1 NM_024523.5 1.377403631 0.345129567 3.16E−13 0.000388553 0 0.00261 607. DOHH NM_031304.3 1.377136426 0.060583272 3.42E−13 0.464259653 0 0.65186 608. ZNF721 NM_133474.2 1.374804369 −0.08379608 2.03E−12 0.359423741 0 0.55546 609. MGC39900 NM_194324.1 1.373970776 −0.60573503 7.17E−13 6.56E−07 0 1.00E−05 610. KCTD5 NM_018992.2 1.373520781 −0.24714681 2.17E−14 0.002096705 0 0.01073 611. CDO1 NM_001801.2 1.372706326 0.115369911 3.98E−13 0.172921753 0 0.33967 612. SNHG1 NR_003098.1 1.372510324 −0.24948274 8.72E−14 0.003479011 0 0.01638 613. RPF1 NM_025065.6 1.372051665 0.218421831 8.46E−13 0.018398193 0 0.06336 614. ZNF408 NM_024741.1 1.371029586 0.061624875 2.76E−13 0.449623929 0 0.63904 615. PFKFB3 NM_004566.2 1.369564991 0.250778898 8.85E−13 0.00802405 0 0.03265 616. C8orf79 NM_020844.2 1.369321582 0.053699642 1.69E−11 0.597484886 0 0.75758 617. ZNF256 NM_005773.2 1.367327098 0.093687711 2.44E−12 0.309062419 0 0.50444 618. VGLL2 NM_153453.1 1.367173619 0.126611023 1.56E−12 0.163851344 0 0.32735 619. CCDC49 NM_017748.3 1.364719391 0.136302741 5.90E−13 0.11587493 0 0.25639 620. AMD1 NM_001033059.1 1.362028458 −0.75667482 5.49E−12 1.11E−07 0 0 621. RAPGEF2 NM_014247.2 1.361231387 0.055181721 2.93E−10 0.642357037 0 0.79015 622. SNORD36A NR_002448.1 1.35930066 0.194368066 2.93E−09 0.162157825 0 0.32489 623. BUD31 NM_003910.2 1.357782326 0.193119675 5.33E−13 0.029005221 0 0.09028 624. FBXL12 NM_017703.1 1.356779609 0.167789916 1.68E−11 0.106231056 0 0.24053 625. SNORD55 NR_000015.2 1.356349401 0.150448175 5.67E−13 0.082334618 0 0.20033 626. KIAA1429 NM_183009.1 1.355815619 0.116182435 2.49E−13 0.154973264 0 0.31506 627. LOC729200 XR_015946.2 1.353808445 0.172309846 1.44E−12 0.059946156 0 0.15783 628. DLEU1 NR_002605.1 1.352475748 −0.34822451 5.08E−13 0.000383086 0 0.00258 629. BAZ1A NM_013448.2 1.352043552 0.403141817 2.65E−13 5.40E−05 0 0.00049 630. TXNDC12 NM_015913.2 1.351366565 −0.2192402 1.23E−12 0.01857404 0 0.06389 631. SDC2 NM_002998.3 1.350110395 −0.08724225 1.56E−12 0.325167328 0 0.52177 632. ROCK1 NM_005406.2 1.34927666 0.148525788 3.50E−12 0.116008557 0 0.25657 633. IER2 NM_004907.2 1.349204584 0.064050022 2.24E−10 0.581064955 0 0.74435 634. MRPL44 NM_022915.2 1.348983987 0.617239832 4.79E−13 2.75E−07 0 1.00E−05 635. HIST2H2BE NM_003528.2 1.347350076 0.271284389 1.02E−13 0.001642357 0 0.00874 636. SRP14P1 NR_003273.1 1.345710532 0.171734899 2.29E−12 0.065389222 0 0.16848 637. C13orf15 NM_014059.2 1.345166905 −0.26286642 1.58E−12 0.006411715 0 0.02713 638. CRHBP NM_001882.3 1.344139949 −0.12281419 8.79E−12 0.209617367 0 0.38827 639. LOC642333 XR_019071.1 1.343692626 0.025090359 1.16E−11 0.796766364 0 0.8907 640. KIAA0922 NM_015196.2 1.342982901 0.04361988 3.17E−12 0.631042252 0 0.78227 641. CAMK2G NM_001222.2 1.341779485 −0.17192793 4.52E−12 0.073983174 0 0.18471 642. TNFRSF10D NM_003840.3 1.340389565 0.140679104 1.35E−11 0.161604163 0 0.32404 643. TC2N NM_152332.3 1.338002738 −0.12357892 2.28E−11 0.228501198 0 0.41174 644. FBX044 NM_001014765.1 1.334510208 −0.03205932 9.53E−11 0.768688418 0 0.87335 645. C1orf182 NM_144627.2 1.333386659 0.214999181 7.85E−12 0.032329912 0 0.09824 646. NRBF2 NM_030759.3 1.330837635 0.047479638 2.06E−12 0.589362968 0 0.75086 647. TMEM119 NM_181724.1 1.330166389 −0.5390834 9.96E−11 6.95E−05 0 0.00061 648. TFAM NM_003201.1 1.32791716 −0.2004992 1.61E−12 0.029119131 0 0.09055 649. ADNP2 NM_014913.2 1.326077627 −0.11379936 3.31E−13 0.160510429 0 0.32288 650. DUX4 NM_033178.1 1.325834384 −0.12775373 6.03E−12 0.178056067 0 0.34639 651. LOC100132418 XM_001719607.1 1.325451904 0.072319727 2.91E−13 0.361714474 0 0.55754 652. FAM89A XM_939093.1 1.324823585 0.485070974 2.01E−11 7.88E−05 0 0.00068 653. DOPEY1 NM_015018.2 1.324238908 −0.00463821 9.57E−13 0.955758726 0 0.97971 654. RPS7 NM_001011.3 1.323525637 0.022583587 1.80E−12 0.794199811 0 0.88916 655. LOC285407 XM_209597.8 1.321959178 −0.17369245 3.54E−10 0.146378753 0 0.30272 656. TRIM36 NM_018700.3 1.321275285 0.009470146 8.39E−11 0.929501366 0 0.96595 657. C5orf27 XR_040299.1 1.320540369 0.154366501 1.77E−09 0.23549402 0 0.42037 658. FAM53C NM_016605.1 1.319296494 −0.17615807 5.63E−12 0.066492472 0 0.17066 659. ACAP2 NM_012287.4 1.317695146 −0.40479958 4.99E−12 0.000227632 0 0.00166 660. LOC653080 XM_925939.1 1.316954224 −0.01245615 6.77E−12 0.893022129 0 0.94527 661. NEDD4 NM_006154.2 1.316933474 −0.03632561 6.83E−12 0.695551993 0 0.82619 662. RBM7 NM_016090.2 1.315671181 0.056243381 1.80E−11 0.566438271 0 0.7341 663. HIST1H2BK NM_080593.1 1.315332973 1.001473221 4.10E−13 5.61E−11 0 0 664. LOC728779 XM_001128458.2 1.313895474 −0.22508026 1.45E−10 0.051226883 0 0.14009 665. SF3B4 NM_005850.3 1.313732124 0.02305885 2.28E−12 0.791135393 0 0.887 666. SNORD95 NR_002591.1 1.310849643 0.196557485 5.32E−13 0.022164576 0 0.07311 667. HIST2H2AC NM_003517.2 1.310148122 0.96312555 1.46E−12 3.47E−10 0 0 668. NCOA7 NM_181782.2 1.308543286 −0.05714471 1.26E−12 0.498253253 0 0.67988 669. SNORD35A NR_000018.1 1.308528091 −0.11569171 4.01E−11 0.262839706 0 0.45307 670. HIST2H2AA4 NM_001040874.1 1.308519368 1.065247493 1.96E−13 8.39E−12 0 0 671. POLB NM_002690.1 1.307319155 −0.10916113 1.26E−13 0.150760489 0 0.30898 672. USPL1 NM_005800.3 1.306587916 0.105879184 6.19E−12 0.254825898 0 0.4433 673. PPP2R5E NM_006246.2 1.306086979 −0.22178951 5.16E−13 0.010766342 0 0.04116 674. APOE NM_000041.2 1.303237847 −0.2177197 5.23E−08 0.171345308 0 0.3376 675. YY1 NM_003403.3 1.303013147 0.502718394 1.51E−11 3.56E−05 0 0.00035 676. TNNC1 NM_003280.1 1.302492998 −0.34243175 4.20E−09 0.01679525 0 0.05887 677. MCCC1 NM_020166.3 1.302246373 −0.12257597 4.12E−13 0.129876892 0 0.27791 678. TAF13 NM_005645.3 1.301676767 0.91664427 9.66E−11 3.40E−08 0 0 679. TCEAL6 NM_001006938.1 1.300207468 0.092987926 1.26E−11 0.331687907 0 0.52832 680. CCNT1 NM_001240.2 1.29946761 0.323578115 1.71E−11 0.002857177 0 0.01389 681. THOC5 NM_001002878.1 1.293641378 0.198067292 1.83E−12 0.028130358 0 0.08812 682. DCLK2 NM_001040260.1 1.292712666 0.001051025 7.33E−12 0.990814815 0 0.99641 683. HIST2H2AA3 NM_003516.2 1.29270342 1.068878593 6.00E−11 1.59E−09 0 0 684. LOC732432 XM_001724189.1 1.29255263 0.356110754 3.60E−13 0.000157208 0 0.0012 685. LOC642414 XR_016151.1 1.292393963 0.080639319 3.68E−12 0.363877307 0 0.55985 686. LOC100128086 XR_039419.1 1.290071693 −0.18490951 6.51E−13 0.029470618 0 0.09135 687. LOC650029 XM_941861.1 1.288588402 −0.15880653 8.82E−12 0.09585711 0 0.22333 688. KLHL11 NM_018143.1 1.28224461 0.481352064 1.15E−11 4.11E−05 0 0.00039 689. CACYBP NM_014412.2 1.281960322 0.100405054 9.02E−12 0.280273125 0 0.47356 690. ZNF207 NM_001032293.2 1.280488078 −0.35384934 1.73E−11 0.00121518 0 0.00676 691. MYH3 NM_002470.2 1.279552852 0.040077269 1.23E−12 0.62562708 0 0.77824 692. LOC100129186 XM_001722466.1 1.276664758 −0.06261277 1.17E−11 0.501268658 0 0.68228 693. RAB8B NM_016530.2 1.274043645 −0.25001293 5.54E−11 0.020865118 0 0.06981 694. UTP6 NM_018428.2 1.273624089 0.077948838 3.39E−13 0.311461608 0 0.50699 695. LOC727759 XM_001125931.1 1.270342079 −0.08623897 1.19E−10 0.415482102 0 0.60841 696. C10orf137 NM_015608.2 1.270304463 −0.2203145 9.39E−11 0.043795827 0 0.1243 697. LHX3 NM_014564.2 1.269639702 0.181228781 1.56E−09 0.148067536 0 0.30529 698. C17orf85 NM_018553.1 1.267776498 −0.34613961 1.81E−12 0.000426416 0 0.00282 699. FAM90A6P XR_016591.1 1.267761321 −0.11675928 2.46E−11 0.231679429 0 0.41577 700. IVNS1ABP NM_006469.4 1.267243547 −0.47174373 4.25E−12 2.34E−05 0 0.00024 701. KIAA0831 NM_014924.3 1.26652451 −0.16734391 1.53E−12 0.05225327 0 0.1423 702. PLS1 NM_002670.1 1.266329601 −0.17494654 1.31E−11 0.069705634 0 0.17675 703. RBM15 NM_022768.4 1.266035304 0.293252074 1.82E−11 0.00503893 0 0.02224 704. ABCE1 NM_001040876.1 1.262588568 −0.26709225 2.32E−12 0.004241556 0 0.01934 705. TMEM126A NM_032273.2 1.261901695 −0.05964487 2.33E−12 0.478764938 0 0.66392 706. ITPR1 NM_002222.4 1.261809954 −0.0147413 1.48E−12 0.856699688 0 0.92516 707. RLF NM_012421.2 1.26115445 0.287736727 4.21E−12 0.003076025 0 0.01476 708. UTP14A NM_006649.2 1.257816378 0.095234161 1.32E−12 0.246855274 0 0.43415 709. LGMN NM_001008530.1 1.256081468 1.113926389 3.67E−10 2.80E−09 0 0 710. RBBP5 NM_005057.2 1.255816476 0.093609057 1.07E−11 0.308046571 0 0.5034 711. CCDC109A NM_138357.1 1.254274908 −0.17212988 7.10E−12 0.062920858 0 0.16362 712. LOC644863 XM_927955.1 1.254068947 0.163338204 6.17E−12 0.074216318 0 0.18513 713. EEF1B2 NM_021121.2 1.248657387 −0.12650563 5.85E−13 0.110892564 0 0.24841 714. PTGR1 NM_012212.2 1.248408075 −0.07406433 1.00E−12 0.353941061 0 0.55047 715. SLC4A7 NM_003615.2 1.246394864 −0.73843401 3.41E−11 1.97E−07 0 0 716. LOC651441 XM_940596.1 1.246244963 0.129210396 5.63E−11 0.200030139 0 0.37594 717. LOC653544 NM_001127388.1 1.245204137 8.133080049 5.52E−12 1.24E−27 0 0 718. WDSOF1 NM_015420.5 1.245112777 0.341385415 8.15E−12 0.000896331 0 0.00527 719. LOC730740 XM_001128558.1 1.245100265 −0.50513988 2.33E−12 5.11E−06 0 7.00E−05 720. MED30 NM_080651.1 1.243913532 −0.04610568 1.20E−12 0.563719573 0 0.73184 721. FASTKD5 NM_021826.4 1.243376527 −0.04083647 5.19E−13 0.592075228 0 0.75304 722. NFKBIB NM_001001716.1 1.241142414 0.16150492 2.67E−11 0.098219921 0 0.22704 723. TDRD3 NM_030794.1 1.241044113 0.158162814 3.16E−10 0.155663666 0 0.31604 724. EAF2 NM_018456.4 1.240601106 0.006357779 2.61E−12 0.938766592 0 0.97063 725. RBM24 NM_153020.1 1.238467184 −0.35037323 7.03E−12 0.000621695 0 0.00387 726. LOC653884 XM_936240.1 1.237831878 0.507599057 1.42E−11 1.62E−05 0 0.00018 727. ZNF644 NM_201269.1 1.237163651 0.1866136 8.64E−13 0.024652802 0 0.07977 728. LOC146517 XM_928464.1 1.23477277 0.12999852 8.73E−13 0.105411256 0 0.23913 729. LTV1 NM_032860.3 1.233857043 0.166110732 1.69E−12 0.049498263 0 0.13639 730. SNRPB NM_003091.3 1.233132452 0.057129747 1.02E−11 0.521802992 0 0.6983 731. C17orf98 NM_001080465.2 1.231755999 −0.1664012 1.23E−08 0.223277849 0 0.40501 732. TUFT1 NM_020127.1 1.231104113 −0.4862346 2.07E−11 3.32E−05 0 0.00033 733. LOC728889 XR_015885.2 1.230896717 −0.31160961 1.89E−10 0.006845006 0 0.02868 734. C10orf2 NM_021830.3 1.229963691 0.212014111 1.82E−11 0.029394954 0 0.09118 735. TPMT NM_000367.2 1.229256548 −0.82629722 2.47E−12 2.58E−09 0 0 736. VGF NM_003378.2 1.228290671 0.144420185 1.36E−11 0.119191485 0 0.2617 737. LOC654121 XM_942442.1 1.227259775 0.572587844 3.06E−11 5.35E−06 0 7.00E−05 738. USP33 NM_201624.1 1.227092095 0.364765018 3.21E−11 0.000864329 0 0.00511 739. NLF2 XM_940314.2 1.225068547 −0.01440261 1.30E−08 0.914278599 0 0.95828 740. EIF1AX NM_001412.3 1.224893472 0.396862112 2.60E−08 0.009416068 0 0.0371 741. DNAJB9 NM_012328.1 1.224559886 0.297230165 7.88E−12 0.002486592 0 0.01233 742. SCYL2 NM_017988.4 1.223376659 0.47495511 6.42E−12 1.85E−05 0 2.00E−04 743. TMED7 NM_181836.3 1.223335413 −0.04749956 2.79E−12 0.563673099 0 0.73182 744. DSP NM_001008844.1 1.223040013 0.42967214 1.91E−12 2.77E−05 0 0.00028 745. TERF2IP NM_018975.2 1.222689453 −0.23536142 4.29E−13 0.004309204 0 0.01959 746. U2AF2 NM_007279.2 1.220559233 0.016936652 8.69E−13 0.825243869 0 0.9073 747. U2AF1 NM_001025203.1 1.219213779 −0.041112 7.40E−12 0.634230121 0 0.7842 748. SNORA63 NR_002586.1 1.219018919 −0.06620908 1.19E−11 0.457454961 0 0.64605 749. HMGB2 NM_002129.2 1.218723322 −0.53026679 1.50E−07 0.002562451 0 0.01264 750. DHX8 NM_004941.1 1.218618843 0.210654498 5.11E−12 0.02013271 0 0.06787 751. DOCK10 NM_014689.2 1.218590663 −0.042392 1.38E−12 0.59054411 0 0.75181 752. LOC144438 NR_024266.1 1.216625995 0.134450249 9.10E−12 0.133366661 0 0.28295 753. WBP11 NM_016312.2 1.215719368 0.398606804 2.78E−13 1.78E−05 0 0.00019 754. PUM1 NM_001020658.1 1.215582613 0.10228495 2.58E−12 0.215979086 0 0.39656 755. PSMD12 NM_002816.3 1.21295595 0.798891424 4.44E−12 6.17E−09 0 0 756. CCDC148 NM_138803.2 1.212800766 0.040306505 1.64E−11 0.653656949 0 0.79782 757. ZCCHC8 NM_017612.2 1.211248515 0.140658038 5.76E−12 0.107274482 0 0.2424 758. DCP1A NM_018403.4 1.210640832 0.495731651 2.96E−12 5.37E−06 0 7.00E−05 759. ARL5B NM_178815.3 1.210545187 −0.09231272 1.11E−11 0.298109633 0 0.49291 760. IMMP2L NM_032549.2 1.209910969 0.118062245 2.12E−12 0.149914058 0 0.30778 761. RFWD3 NM_018124.3 1.208049138 −0.11579668 1.10E−12 0.142978067 0 0.2976 762. C20orf7 NM_024120.3 1.206932447 −0.02172869 1.68E−11 0.807832173 0 0.89708 763. SCML2 NM_006089.1 1.206323289 −0.07204003 1.79E−11 0.424905947 0 0.6166 764. FBXL20 NM_032875.1 1.205956758 0.454990439 1.72E−10 0.000214189 0 0.00157 765. LOC653541 XM_927996.1 1.20581303 7.882897275 3.07E−11 7.96E−27 0 0 766. DCP2 NM_152624.4 1.204056822 −0.3465364 2.71E−10 0.003144443 0 0.01504 767. LOC388796 NR_015366.2 1.20284251 0.039131411 7.49E−11 0.686674781 0 0.82025 768. LOC652051 XM_945171.1 1.201518638 −0.07496917 2.53E−09 0.529864774 0 0.70492 769. CYB5R4 NM_016230.3 1.197397531 0.349078413 1.06E−09 0.005162324 0 0.0227 770. NOMO3 NM_001004067.2 1.195932458 0.046354378 1.14E−12 0.545034581 0 0.71717 771. FRG2 NM_001005217.1 1.193331745 0.021093081 5.12E−10 0.844224234 0 0.91796 772. BCYRN1 NR_001568.1 1.193135044 −0.22422137 2.53E−11 0.020757969 0 0.06948 773. LOC728732 XR_015658.2 1.19197695 −0.38091713 1.54E−09 0.003075392 0 0.01476 774. RPS24 NM_001026.3 1.191834275 −0.02375199 1.55E−12 0.758786803 0 0.86777 775. LOC729101 XR_015731.1 1.191021556 0.08489762 1.84E−11 0.34338919 0 0.54043 776. C16orf91 NM_001010878.1 1.190020554 0.224307109 4.30E−12 0.011584594 0 0.0437 777. FAM32A NM_014077.2 1.189895447 −0.36437445 5.59E−12 0.000251167 0 0.0018 778. ARGLU1 NM_018011.3 1.189872383 −0.44077423 2.68E−12 1.81E−05 0 2.00E−04 779. PDE12 NM_177966.4 1.189087195 −0.24628904 7.81E−12 0.007852276 0 0.0321 780. NUDT1 NM_198948.1 1.186929197 −0.60529807 1.46E−11 8.85E−07 0 2.00E−05 781. ZNF197 NM_001024855.1 1.185963019 0.065216551 5.25E−09 0.595754477 0 0.75601 782. RWDD1 NM_016104.2 1.185820615 0.212048388 5.90E−11 0.033857374 0 0.10179 783. GABPB2 NM_016655.3 1.185669017 0.622815689 8.22E−11 2.29E−06 0 4.00E−05 784. PPTC7 NM_139283.1 1.18504186 0.377800479 1.22E−12 6.51E−05 0 0.00058 785. C16orf33 NM_024571.2 1.184672145 −0.28869785 4.23E−13 0.000592512 0 0.00372 786. EZH2 NM_004456.3 1.18450651 −0.09718009 1.20E−10 0.327044721 0 0.52385 787. CLK3 NM_003992.1 1.182797695 0.143529638 9.16E−11 0.147062855 0 0.30375 788. C6orf211 NM_024573.1 1.182525121 −0.12028548 9.63E−12 0.166541987 0 0.33151 789. PPHLN1 NM_201438.1 1.180946148 −0.0874507 4.44E−11 0.3487725 0 0.54521 790. CCT2 NM_006431.2 1.18058187 −0.04058786 1.04E−11 0.634135173 0 0.7842 791. RYK NM_002958.3 1.180514518 0.034025682 7.51E−12 0.68423347 0 0.81863 792. RNF38 NM_022781.4 1.180119761 −0.31966537 2.57E−12 0.000554487 0 0.00352 793. FOSB NM_006732.1 1.18009734 0.065219396 4.78E−11 0.483952007 0 0.66799 794. 3-Mar NM_178450.2 1.179405566 −0.14780229 8.75E−12 0.090635754 0 0.2146 795. F13A1 NM_000129.3 1.179334053 −0.22849384 4.00E−12 0.009520136 0 0.03736 796. UTP23 NM_032334.1 1.179003856 0.169136319 8.46E−11 0.088424102 0 0.21095 797. ADAT3 NM_138422.1 1.17865106 0.161462572 1.85E−12 0.046975442 0 0.13112 798. IMPA1 NM_005536.2 1.178227788 −0.08075737 7.92E−10 0.46062656 0 0.64874 799. RAE1 NM_003610.3 1.178175402 0.092187439 2.08E−11 0.302608212 0 0.49776 800. FKBP14 NM_017946.2 1.177647758 0.034851434 9.59E−12 0.68041316 0 0.81551 801. LOC653555 XM_930357.1 1.177450046 −0.10106816 1.38E−11 0.248889707 0 0.43674 802. CHD2 NM_001042572.2 1.177393315 0.536849393 1.23E−11 3.66E−06 0 5.00E−05 803. LBH XM_001132517.1 1.176505407 0.146755689 1.52E−10 0.147661982 0 0.30468 804. LPAR2 NM_004720.5 1.176329258 −0.19958741 5.99E−10 0.073078115 0 0.18312 805. UTX NM_021140.1 1.175093332 0.368146383 1.77E−12 9.97E−05 0 0.00082 806. C21orf66 NM_013329.3 1.174366312 0.227324159 5.18E−12 0.010471937 0 0.04028 807. PKN2 NM_006256.2 1.173284488 0.376740622 7.94E−10 0.002174139 0 0.01104 808. NCRNA00120 NR_002767.1 1.173282961 0.154729511 3.69E−11 0.099773325 0 0.22967 809. PAMR1 NM_015430.2 1.172030741 −0.53596645 6.27E−10 5.90E−05 0 0.00053 810. HNRNPF NM_001098204.1 1.171885264 0.04829931 9.03E−12 0.565705988 0 0.73349 811. SESTD1 NM_178123.3 1.171845532 0.559779016 1.09E−10 1.01E−05 0 0.00012 812. KIAA1370 NM_019600.1 1.170437676 0.222026045 5.61E−08 0.124466191 0 0.26955 813. DUX5 NM_012149.2 1.169110122 8.352310262 2.85E−11 1.29E−27 0 0 814. H2AFX NM_002105.2 1.168526313 −0.40973461 9.73E−11 0.000324394 0 0.00224 815. LOC151162 NR_024275.1 1.168361058 −0.52040882 1.72E−11 6.42E−06 0 8.00E−05 816. FLNA NM_001456.2 1.166988048 −0.15565008 2.63E−08 0.250549307 0 0.43867 817. KLC2 XM_942434.1 1.166725495 −0.05195465 3.31E−11 0.5639232 0 0.73198 818. Cxorf40B NM_001013845.1 1.165126358 −0.20340904 1.58E−12 0.013176463 0 0.04859 819. LOC649679 XM_945045.1 1.164608362 −0.10676387 4.20E−11 0.247388043 0 0.43485 820. YTHDF3 NM_152758.4 1.163867955 −0.54389276 1.72E−10 1.85E−05 0 2.00E−04 821. WDR1 NM_017491.3 1.162128671 0.314399308 4.57E−12 0.000755102 0 0.00456 822. GPR137C NM_001099652.1 1.162065847 −0.14626927 1.18E−11 0.094311309 0 0.22079 823. ZNF280C NM_017666.2 1.16196573 −0.30812714 5.93E−11 0.003022016 0 0.01456 824. SNRPA1 NM_003090.2 1.160234865 −0.0971834 6.59E−13 0.185745052 0 0.35735 825. LOC731314 XM_001129173.1 1.160171401 −0.59088551 1.13E−11 7.32E−07 0 1.00E−05 826. WDR33 NM_001006623.1 1.159819745 0.034425292 1.90E−09 0.760249381 0 0.86846 827. KIAA0174 NM_014761.2 1.159746034 0.094593398 1.03E−11 0.264976548 0 0.45596 828. CCNYL1 NM_152523.1 1.158021572 0.324086783 4.91E−11 0.001799583 0 0.00944 829. ZSCAN5A NM_024303.1 1.157005262 0.099010624 2.61E−10 0.328308092 0 0.52502 830. RQCD1 NM_005444.1 1.156902459 0.284534409 3.03E−11 0.004009816 0 0.01845 831. SYT14 NM_153262.1 1.155984015 −0.05094428 1.16E−09 0.641268115 0 0.78936 832. ZFP37 NM_003408.1 1.154571801 −0.15669228 5.15E−12 0.061327996 0 0.16062 833. LOC100132715 XR_039129.1 1.153897859 −0.59825112 1.23E−10 3.76E−06 0 5.00E−05 834. ARPC5L NM_030978.1 1.153323166 0.192210575 1.00E−11 0.02941857 0 0.09121 835. EIF2C3 NM_024852.2 1.153143186 0.088701042 5.10E−10 0.396584237 0 0.5905 836. LOC648218 XR_038470.1 1.15300723 0.116219282 5.04E−09 0.333733818 0 0.53075 837. ERMP1 NM_024896.2 1.152922839 −0.34213368 1.83E−10 0.002063249 0 0.01058 838. SLC25A26 NM_173471.2 1.1527525 0.107031552 4.80E−11 0.245026441 0 0.43181 839. LOC100134229 NR_024451.1 1.151548683 −0.07008176 1.95E−11 0.418539839 0 0.61073 840. PDZD8 NM_173791.3 1.150893598 0.690707165 9.87E−11 3.99E−07 0 1.00E−05 841. CAMSAP1 NM_015447.1 1.150184828 −0.29416462 5.42E−11 0.003828029 0 0.01777 842. GRPEL2 NM_152407.3 1.149277281 −0.34708288 3.43E−12 0.000219119 0 0.0016 843. ATXN1L NM_001137675.2 1.149100267 0.160679583 1.60E−11 0.069529635 0 0.17643 844. JARID1A NM_005056.1 1.148694966 0.660170132 3.60E−11 3.25E−07 0 1.00E−05 845. HACL1 NM_012260.2 1.148242322 0.170042244 5.42E−13 0.023782023 0 0.07753 846. LOC652864 XM_942571.1 1.147835016 0.251953952 3.58E−12 0.003853529 0 0.01786 847. DNAJA2 NM_005880.2 1.147267377 −0.33265979 7.18E−12 0.000497232 0 0.00321 848. NARG2 NM_024611.4 1.146741454 0.176576894 3.88E−10 0.093477893 0 0.21943 849. MRPL4 NM_146387.1 1.145647285 −0.02282466 1.17E−10 0.80945376 0 0.89811 850. LOC402112 XR_038697.1 1.144036715 −0.3090144 2.74E−09 0.012338231 0 0.04605 851. RBM25 NM_021239.1 1.143184414 −0.7474824 4.09E−10 3.77E−07 0 1.00E−05 852. LOC440957 NM_001124767.1 1.142658371 −0.11333951 1.30E−11 0.183800864 0 0.35459 853. RBM4 NM_002896.2 1.142534032 −0.12535865 3.80E−12 0.118666169 0 0.26092 854. DOCK7 NM_033407.2 1.141715883 0.120684314 2.54E−11 0.173016832 0 0.33974 855. MTAP NM_002451.3 1.141530828 −0.42200093 4.84E−11 0.00012275 0 0.00098 856. SPRY2 NM_005842.2 1.141246432 0.116007546 1.52E−11 0.17724193 0 0.34566 857. SGSH NM_000199.2 1.141108849 −0.07693406 2.86E−11 0.381155146 0 0.57683 858. PSME4 NM_014614.1 1.1409872 −0.13684263 6.12E−12 0.098020161 0 0.2267 859. SNRPD3 NM_004175.3 1.140784492 −0.40231415 1.57E−11 0.000102598 0 0.00084 860. CDC20 NM_001255.2 1.140182998 −1.05610107 1.68E−11 6.52E−11 0 0 861. TAPT1 NM_153365.2 1.13931014 −0.29519427 8.03E−12 0.0014642 0 0.00792 862. IL34 NM_152456.1 1.13658319 −0.15420528 1.03E−11 0.071015728 0 0.17933 863. KIF5C NM_004522.1 1.136063506 0.284965136 2.62E−12 0.001132059 0 0.00638 864. SNORD46 NR_000024.2 1.135886497 0.126491002 7.94E−11 0.178079469 0 0.34639 865. LOC650681 XM_939769.1 1.135843324 0.252741513 1.16E−07 0.087843276 0 0.20994 866. SDHD NM_003002.1 1.135547623 0.16981842 6.16E−11 0.071811562 0 0.18078 867. UTP3 NM_020368.1 1.13507536 −0.01605332 8.34E−10 0.878544114 0 0.93721 868. SFRS13A NM_054016.1 1.132010092 0.346810466 4.77E−12 0.000228251 0 0.00166 869. RAPGEF6 NM_016340.4 1.131041131 −0.20229021 2.62E−10 0.049371237 0 0.13613 870. BNIP2 NM_004330.1 1.1307605 0.058327397 4.16E−11 0.509960162 0 0.68865 871. LOC100129585 XM_001720509.1 1.130482384 −0.33768311 4.22E−11 0.000950757 0 0.00553 872. ACTR6 NM_022496.3 1.130266859 0.2078082 3.36E−10 0.046720379 0 0.13056 873. SNORD3D NR_006882.1 1.129349989 −0.15047088 1.78E−09 0.178731436 0 0.34738 874. PCDH7 NM_002589.2 1.129103025 −0.11725418 1.88E−11 0.173317449 0 0.34017 875. ZFAND2A NM_182491.1 1.127598591 0.424216292 1.71E−10 0.000219516 0 0.0016 876. C18orf19 NM_152352.1 1.125760245 0.576124294 9.33E−11 3.61E−06 0 5.00E−05 877. CD55 NM_000574.2 1.125583524 0.09757057 1.65E−08 0.437689181 0 0.62834 878. ORC6L NM_014321.2 1.124086663 −0.25724434 1.59E−10 0.012257872 0 0.04578 879. C9orf72 NM_018325.1 1.123974845 −0.05500311 1.48E−10 0.560325102 0 0.72912 880. GART NM_175085.1 1.121272949 −0.0022074 1.25E−10 0.981050813 0 0.9915 881. C2orf25 NM_015702.1 1.120641663 0.203618336 2.79E−11 0.025460046 0 0.08178 882. DNAJC12 NM_201262.1 1.12040563 −0.0362982 2.42E−10 0.707153619 0 0.83337 883. USP38 NM_032557.4 1.119769951 −0.22060385 1.71E−11 0.014090426 0 0.05121 884. C12orf43 NM_022895.1 1.119308684 0.090747708 7.53E−11 0.320137982 0 0.51653 885. KIAA1553 XM_166320.6 1.118336577 −0.16362906 3.17E−10 0.105928992 0 0.24001 886. CCNE2 NM_057735.1 1.118143253 −0.54142828 2.03E−10 1.34E−05 0 0.00015 887. LOC440013 XM_495854.3 1.117710485 −0.11283821 1.12E−09 0.290476588 0 0.48528 888. HSPC111 NM_016391.3 1.11521876 −0.08294349 4.69E−11 0.348179771 0 0.54481 889. CROP NM_006107.2 1.115120822 −0.02390027 1.42E−08 0.845309646 0 0.91816 890. LOC650659 XM_939743.1 1.114062456 −0.018238 1.51E−10 0.845164054 0 0.91816 891. TOP1P2 NR_001283.1 1.113709756 0.457354204 1.29E−08 0.001124671 0 0.00635 892. INA NM_032727.2 1.113095856 0.371877537 1.20E−10 0.000585691 0 0.00368 893. SNORD96A NR_002592.1 1.111980201 0.173882795 7.81E−11 0.063957759 0 0.16557 894. CTGF NM_001901.1 1.108704726 0.048757922 1.47E−10 0.600387669 0 0.75992 895. PELO NM_015946.4 1.107903729 0.447764627 2.19E−11 2.61E−05 0 0.00027 896. FAM13B NM_001101800.1 1.107074212 −0.39747766 2.19E−11 0.000103456 0 0.00084 897. SECISBP2L NM_014701.2 1.106578146 −0.22306548 2.00E−10 0.026538534 0 0.0843 898. PTRH2 NM_016077.3 1.106198027 0.051646279 5.30E−10 0.60554211 0 0.76362 899. ZNF326 NM_182976.1 1.105462864 0.089833502 1.60E−09 0.402361041 0 0.59572 900. MRPS22 NM_020191.2 1.104391719 0.137510836 5.48E−12 0.084902738 0 0.20478 901. ETFA NM_000126.2 1.104011525 −0.11194638 3.10E−12 0.143171588 0 0.29776 902. UBE2C NM_181800.1 1.103795231 −0.66378591 1.29E−11 6.81E−08 0 0 903. CPEB4 NM_030627.1 1.103538487 −0.04915988 6.54E−10 0.626317192 0 0.77881 904. LRIG1 NM_015541.2 1.103069438 −0.3892228 9.87E−12 7.63E−05 0 0.00066 905. MTERFD1 NM_015942.3 1.101609269 0.203037686 8.82E−12 0.016698947 0 0.05858 906. RNF11 NM_014372.3 1.100921921 0.80070928 3.32E−12 9.01E−10 0 0 907. API5 NM_006595.2 1.100005738 −0.35541321 7.13E−11 0.000606078 0 0.00379 908. LOC100008589 NR_003287.1 1.099836345 0.013221676 2.48E−11 0.87371699 0 0.93459 909. TMEM41B NM_015012.1 1.099587778 −0.06296624 3.71E−12 0.404057125 0 0.59754 910. DISCI NM_018662.2 1.099547571 0.009834467 5.62E−09 0.931273035 0 0.96692 911. POLR2C NM_032940.2 1.099528324 0.144651532 2.39E−11 0.092968286 0 0.21857 912. MELK NM_014791.2 1.099204313 0.005893628 7.72E−11 0.946978282 0 0.97421 913. CSPP1 NM_024790.5 1.098156009 −0.29171614 1.19E−11 0.001427133 0 0.00775 914. ZFAND6 NM_019006.2 1.098143704 0.121576691 5.23E−09 0.290628354 0 0.48546 915. LOC645159 XM_928195.2 1.097335884 0.343566046 2.37E−09 0.004355571 0 0.01976 916. NUP35 NM_138285.3 1.096524096 0.241203379 8.35E−12 0.005336103 0 0.02329 917. C4orf32 NM_152400.1 1.096395353 −0.14449188 7.12E−11 0.112146071 0 0.25035 918. TIPIN NM_017858.1 1.096292861 0.336263475 1.87E−11 0.0004838 0 0.00315 919. MTMR14 NM_001077525.1 1.096198232 −0.19881486 5.91E−08 0.142124407 0 0.2961 920. AHSA1 NM_012111.1 1.095960996 0.112980245 1.28E−10 0.223001167 0 0.40477 921. FAM91A1 NM_144963.2 1.095803947 1.249135004 5.30E−10 5.44E−11 0 0 922. MTX3 NM_001010891.3 1.095417954 −0.06931404 5.25E−11 0.426238402 0 0.61793 923. DYSF NM_003494.2 1.095135096 −0.70362085 7.27E−12 1.44E−08 0 0 924. SDCBP NM_001007067.1 1.094876133 0.74649087 1.94E−10 1.05E−07 0 0 925. GOLGB1 NM_004487.3 1.093155626 0.047716974 3.07E−11 0.570009169 0 0.73687 926. TTC14 NM_001042601.1 1.093029226 0.120133704 4.48E−09 0.289652805 0 0.48427 927. LOC651959 XM_941245.2 1.092888624 −0.09423409 6.22E−11 0.286093964 0 0.48037 928. DNTT NM_001017520.1 1.09144065 −0.0043337 5.52E−10 0.964932011 0 0.98418 929. MATR3 NM_199189.1 1.089506951 0.31286756 1.78E−09 0.007094557 0 0.02955 930. FAM108B1 NM_016014.2 1.089500547 0.279342324 1.19E−09 0.012538681 0 0.0467 931. BMP4 NM_130851.1 1.089143839 0.157561736 3.83E−11 0.073449004 0 0.1837 932. RBP1 NM_002899.2 1.08832098 −0.50985444 2.41E−09 0.000110487 0 0.00089 933. PDCL3 NM_024065.3 1.088070063 0.022658241 6.04E−09 0.841613833 0 0.91659 934. CBLL1 NM_024814.1 1.088060901 0.833493724 3.99E−11 3.87E−09 0 0 935. LOC100130856 XM_001726438.1 1.086766448 0.072716194 2.91E−11 0.385084323 0 0.58059 936. ALKBH1 NM_006020.2 1.086751593 0.167891316 6.47E−12 0.037531806 0 0.1103 937. LOC728643 NR_003277.1 1.086411108 −0.63353437 7.06E−11 4.59E−07 0 1.00E−05 938. FLRT3 NM_198391.1 1.085370713 −0.50650589 5.46E−11 8.20E−06 0 1.00E−04 939. PPP2CA NM_002715.2 1.085290607 −0.84059439 7.68E−12 6.81E−10 0 0 940. KITLG NM_000899.3 1.085131721 −0.48718124 6.85E−11 1.58E−05 0 0.00018 941. LOC729608 XM_001714722.1 1.084391366 0.427810224 7.62E−11 7.94E−05 0 0.00068 942. NHP2L1 NM_001003796.1 1.083998244 0.280628365 1.74E−10 0.005678718 0 0.02454 943. HIATL1 NM_032558.2 1.083841715 0.127406235 1.27E−11 0.118068169 0 0.25999 944. NRAS NM_002524.2 1.081779536 0.507268201 4.41E−09 0.00016224 0 0.00124 945. LCOR NM_032440.1 1.081170798 0.153373454 9.61E−10 0.13951058 0 0.29203 946. STIM2 NM_020860.2 1.081169785 0.139486813 3.27E−10 0.15164717 0 0.31037 947. C20orf4 NM_015511.3 1.08024455 0.122711085 9.11E−12 0.123485859 0 0.26817 948. TNNT2 NM_001001431.1 1.078937179 −1.30374985 7.68E−08 3.69E−09 0 0 949. CDKN1A NM_078467.1 1.078195342 0.61217478 1.54E−09 7.94E−06 0 1.00E−04 950. FOS NM_005252.2 1.077938553 0.471813546 5.00E−08 0.001353374 0 0.0074 951. TRAPPC6B NM_001079537.1 1.07714553 0.620681475 7.18E−10 3.59E−06 0 5.00E−05 952. DIP2B NM_173602.2 1.076215614 −0.22003106 1.45E−09 0.042790054 0 0.12221 953. LOC100128266 XR_037888.1 1.075894157 0.090683001 5.06E−11 0.291263966 0 0.48606 954. UBXN7 NM_015562.1 1.075123071 0.303669543 2.10E−11 0.001102216 0 0.00624 955. LOC649137 XM_001131980.1 1.074657889 0.086009469 1.90E−11 0.289591841 0 0.48427 956. PLAGL2 NM_002657.2 1.074636945 −0.10608532 1.23E−11 0.18446662 0 0.35553 957. ENC1 NM_003633.1 1.073105121 −0.28244281 1.61E−10 0.00488697 0 0.0217 958. CS NM_004077.2 1.071166193 −0.32349921 2.04E−11 0.000588363 0 0.0037 959. TSC1 NM_000368.3 1.070718233 0.132984568 2.53E−10 0.160748993 0 0.32322 960. SNHG12 NR_024127.1 1.069391677 0.173833734 1.61E−09 0.102695845 0 0.23446 961. MAPRE3 NM_012326.2 1.068880559 0.12586366 6.94E−11 0.152556734 0 0.31178 962. ZNF509 NM_145291.2 1.068683005 0.044510129 2.47E−10 0.629930314 0 0.78167 963. NAF1 NM_138386.1 1.068629462 0.14733421 8.56E−11 0.100810151 0 0.23132 964. BRPF3 NM_015695.2 1.066813315 −0.0421277 1.19E−11 0.587612568 0 0.74952 965. HDAC2 NM_001527.2 1.066502454 0.013464456 1.00E−10 0.877414192 0 0.93679 966. LOC652874 XM_942590.1 1.066391837 0.005987456 2.58E−09 0.954742823 0 0.9788 967. ZMYM5 NM_001039650.1 1.0652354 0.06857313 8.66E−11 0.431333338 0 0.6223 968. GALM NM_138801.1 1.06343722 0.000591631 8.74E−12 0.993776069 0 0.99739 969. UPF2 NM_080599.1 1.063309533 0.174018826 8.51E−10 0.088977545 0 0.21178 970. ZFP91 NM_053023.3 1.061621244 0.533426555 3.95E−09 7.03E−05 0 0.00061 971. NUP153 NM_005124.2 1.059886645 −0.07908733 1.79E−10 0.382448966 0 0.57803 972. PRPF3 NM_004698.1 1.058354904 0.122657814 3.09E−11 0.141136078 0 0.2945 973. LOC646786 XM_929738.1 1.0577539 0.092682481 1.41E−09 0.363633182 0 0.5596 974. PRPF38A NM_032864.3 1.057666912 −0.17014044 8.89E−10 0.094963043 0 0.22176 975. LOC647081 XR_017490.2 1.057295145 0.08645715 1.22E−10 0.329087945 0 0.52586 976. LOC643509 XM_932666.2 1.057259344 0.004510543 1.11E−08 0.96851601 0 0.98597 977. RN7SK NR_001445.1 1.055974111 0.467639661 3.45E−08 0.00099303 0 0.00573 978. LOC641844 XR_018036.2 1.055485991 0.034857969 4.64E−11 0.673977402 0 0.81163 979. LOC729120 XM_001133026.1 1.054623336 −0.01773804 1.03E−10 0.837515158 0 0.9142 980. KHSRP NM_003685.2 1.053086053 0.175919484 2.53E−10 0.064293983 0 0.16625 981. LOC645691 XM_928701.3 1.052836096 −0.43820017 3.08E−08 0.001599259 0 0.00855 982. ZFYVE1 NM_021260.1 1.051285604 0.133970068 5.62E−11 0.119019359 0 0.26142 983. SYAP1 NM_032796.2 1.050864137 0.498717647 4.36E−09 0.000141491 0 0.0011 984. LOC644877 XR_017355.2 1.050610394 0.090333661 4.83E−11 0.280687722 0 0.47387 985. LOC647037 XM_930029.1 1.050461424 0.115257018 6.54E−11 0.179670227 0 0.34878 986. FAM103A1 NM_031452.2 1.049593448 0.548964175 1.41E−09 2.10E−05 0 0.00022 987. FLRT2 NM_013231.4 1.048015868 −0.5218431 1.47E−10 7.35E−06 0 9.00E−05 988. NUP155 NM_153485.1 1.047710989 0.074659225 2.47E−10 0.412428516 0 0.60612 989. SLC25A38 NM_017875.1 1.047432233 −0.01502885 3.29E−11 0.851906405 0 0.92211 990. SNRPB2 NM_198220.1 1.046529006 −0.01035738 8.35E−11 0.902747873 0 0.95146 991. AZIN1 NM_015878.4 1.046116284 0.275367926 7.12E−10 0.008801689 0 0.03517 992. LOC729920 NM_001101426.2 1.044490551 0.182331537 8.67E−12 0.022336598 0 0.07357 993. FAM176A NM_001135032.1 1.043068124 0.679565693 9.32E−11 1.11E−07 0 0 994. BTBD7 NM_018167.3 1.042663787 0.076298792 4.05E−10 0.413418603 0 0.60671 995. DIRC2 NM_032839.1 1.042199441 0.33518563 3.81E−11 0.000450503 0 0.00295 996. LOC642268 XM_930669.1 1.042113396 0.093744876 4.75E−08 0.450937945 0 0.64012 997. PRICKLE1 NM_153026.1 1.0419728 −0.32716061 8.88E−10 0.002741031 0 0.01338 998. RSL1D1 NM_015659.2 1.041324635 0.198372858 2.86E−11 0.020013413 0 0.06755 999. LOC647150 XR_017449.2 1.041135995 0.401698852 2.58E−10 0.000216086 0 0.00158 1000. HK2 NM_000189.4 1.040582509 0.756005024 6.67E−12 1.76E−09 0 0 1001. ZNF280B NM_080764.2 1.040377213 −0.34290809 1.03E−10 0.000612546 0 0.00382 1002. LOC648210 XR_018923.1 1.040288367 −0.54383326 6.96E−08 0.000313357 0 0.00217 1003. RECQL NM_032941.1 1.040035529 0.682791422 4.19E−11 4.86E−08 0 0 1004. C7orf40 NR_003697.1 1.039297922 0.254352266 1.25E−08 0.034232718 0 0.10265 1005. PABPC4L NM_001114734.1 1.039177821 −0.28475758 2.21E−10 0.004165504 0 0.01904 1006. RIF1 NM_018151.3 1.038795437 0.25544696 2.27E−10 0.008885581 0 0.0354 1007. MYC NM_002467.3 1.037900386 0.3695377 3.03E−11 0.000138606 0 0.00108 1008. LOC652481 XM_941942.1 1.037532026 0.112115526 1.14E−09 0.259332229 0 0.44874 1009. ARMC5 NM_024742.1 1.037457586 0.079707127 3.61E−10 0.387807213 0 0.58317 1010. C4orf39 NM_153027.1 1.037314675 −0.01489551 2.43E−10 0.867606731 0 0.93093 1011. LRRC42 NM_052940.3 1.035624329 −0.04027074 8.03E−11 0.631371597 0 0.78245 1012. SLC25A25 NM_052901.2 1.035390695 −0.43420388 4.21E−11 2.61E−05 0 0.00027 1013. CIRH1A NM_032830.1 1.034638884 0.162219004 1.91E−11 0.045901428 0 0.12876 1014. NOMO1 NM_014287.3 1.034361189 0.020524855 1.37E−08 0.856292177 0 0.92479 1015. LOC649167 XM_938236.1 1.03294322 −0.00095784 1.72E−08 0.993340796 0 0.99732 1016. UTP11L NM_016037.2 1.03253166 0.126861343 1.01E−10 0.144427742 0 0.29971 1017. FAM126B NM_173822.2 1.03203744 0.210382913 3.07E−11 0.013978022 0 0.05093 1018. OTUD6B NM_016023.2 1.03061043 −0.25011699 2.20E−10 0.009555644 0 0.03747 1019. OCIAD2 NM_152398.2 1.030571051 0.27354447 1.58E−09 0.011237412 0 0.04266 1020. OVOL1 XM_001129344.1 1.029828388 −0.05407431 1.62E−10 0.534543893 0 0.70883 1021. MAK10 NM_024635.3 1.029561675 0.263536187 1.23E−10 0.005344587 0 0.02332 1022. C12orf35 NM_018169.2 1.029288164 0.138049248 1.28E−09 0.168036349 0 0.33326 1023. TROVE2 NM_001042370.1 1.028979236 0.169282342 5.63E−10 0.080488255 0 0.197 1024. LOC648638 XM_937706.1 1.028567866 0.223742233 2.87E−11 0.009165968 0 0.03628 1025. LOC642812 XR_036892.1 1.028443066 0.256454233 2.83E−10 0.008820126 0 0.03521 1026. HNRNPAB NM_031266.2 1.026350617 −0.24070782 7.90E−11 0.008160613 0 0.03309 1027. LOC643167 XR_038497.1 1.026257842 0.228448193 3.03E−11 0.008047914 0 0.03272 1028. HIST1H4H NM_003543.3 1.025732011 1.2313351 3.41E−10 1.38E−11 0 0 1029. YTHDC1 NM_001031732.2 1.025117772 0.182849261 2.04E−10 0.04700437 0 0.13117 1030. CD2AP NM_012120.2 1.025051265 −0.01299116 6.14E−10 0.889108296 0 0.94308 1031. C16orf61 NM_020188.2 1.024443103 −0.25843268 7.05E−12 0.001726012 0 0.00912 1032. ZMAT2 NM_144723.1 1.024373429 0.172328577 7.71E−12 0.026128565 0 0.08343 1033. C12orf31 NM_032338.2 1.024231622 −0.0757358 8.37E−10 0.428059074 0 0.61989 1034. GTF2A2 NM_004492.1 1.02237211 −0.198989 1.42E−10 0.028671893 0 0.08945 1035. LOC100132528 XR_038720.1 1.022350592 −0.74065639 4.22E−10 8.24E−08 0 0 1036. TOMM40 NM_006114.1 1.022228207 −0.08335431 4.55E−11 0.303971739 0 0.49905 1037. YWHAE NM_006761.3 1.021995926 −0.09076355 4.35E−10 0.324800606 0 0.52151 1038. SNAPC2 NM_003083.2 1.021301486 −0.05465569 1.50E−09 0.577920709 0 0.74199 1039. TRO NM_001039705.1 1.021058495 −0.22973069 2.00E−11 0.006408205 0 0.02713 1040. STIP1 NM_006819.1 1.019923878 −0.12480443 2.66E−11 0.118431632 0 0.26054 1041. GOLPH4 NM_014498.2 1.018008616 0.715057288 1.96E−10 6.70E−08 0 0 1042. URB2 NM_014777.2 1.0167874 −0.28830611 1.06E−11 0.000752289 0 0.00455 1043. TRK1 NR_001449.1 1.016402194 0.06997919 1.82E−09 0.480194904 0 0.66512 1044. ZDHHC14 NM_024630.2 1.016284079 0.084770694 9.91E−09 0.440766133 0 0.63111 1045. FAM90A18 XM_496955.4 1.015859899 0.065543358 2.28E−09 0.513587831 0 0.69157 1046. LOC100130550 XR_037892.1 1.015722289 0.533948234 1.71E−09 2.27E−05 0 0.00024 1047. LOC730153 XM_001717676.1 1.015289849 −0.00504612 3.32E−11 0.948440233 0 0.97509 1048. HNRNPA1 NM_031157.2 1.014750875 −0.42094853 2.92E−11 2.32E−05 0 0.00024 1049. COX10 NM_001303.2 1.014240958 −0.05259565 5.17E−11 0.512849102 0 0.69087 1050. LOC728022 XM_001720082.1 1.014197516 −0.20136281 7.68E−09 0.07187497 0 0.18088 1051. CENPN NM_018455.3 1.013635291 0.001233995 2.88E−11 0.987260072 0 0.99438 1052. CTDSPL2 NM_016396.2 1.013554506 0.353555626 2.36E−10 0.000562438 0 0.00356 1053. TRMT11 NM_001031712.2 1.01294925 −0.06262036 2.60E−11 0.418764287 0 0.61097 1054. RPF2 NM_032194.1 1.011426861 0.492183836 2.84E−10 1.60E−05 0 0.00018 1055. SLC25A36 NM_018155.1 1.009418195 0.308796337 1.94E−09 0.004729358 0 0.02114 1056. DPM1 NM_003859.1 1.008124946 0.013439446 2.82E−10 0.878048978 0 0.93691 1057. RNU6-15 NR_028372.1 1.00785758 0.710506662 1.87E−10 6.07E−08 0 0 1058. LOC100133950 XM_001721634.1 1.007465188 −0.14119302 1.60E−08 0.214330739 0 0.3943 1059. U2AF1L2 NM_005089.1 1.00671488 0.144171307 8.07E−11 0.088145085 0 0.21044 1060. LOC651864 XM_944981.1 1.006372187 0.013469472 4.00E−09 0.895197227 0 0.94682 1061. SSR2 XM_945430.1 1.006216181 0.009945239 4.38E−10 0.911682417 0 0.95632 1062. SFT2D2 NM_199344.1 1.005497503 0.367781793 1.58E−10 0.000279846 0 0.00197 1063. BCL2L11 NM_006538.3 1.005369308 0.161087859 3.24E−09 0.121645079 0 0.26556 1064. ILF3 NM_004516.2 1.004527624 −0.20420779 1.11E−10 0.02135674 0 0.07109 1065. FAM90A15 XM_001726945.1 1.004342636 0.009238588 6.36E−10 0.919542528 0 0.96147 1066. GADD45B NM_015675.2 1.003484506 0.350422477 1.44E−10 0.00042227 0 0.0028 1067. PSPC1 NM_001042414.1 1.002965925 −0.24270314 1.31E−08 0.036522764 0 0.10799 1068. IDI1 NM_004508.2 1.002827597 −0.21356264 1.19E−09 0.033719799 0 0.10147 1069. TAF9 NM_001015891.1 1.00218608 0.314494729 3.89E−09 0.005311051 0 0.0232 1070. DUSP6 NM_022652.2 1.00169102 0.274501313 1.07E−09 0.00790461 0 0.03227 1071. RBM28 NM_018077.1 1.001253323 0.371778522 5.49E−10 0.000493853 0 0.0032 1072. ACTR5 NM_024855.3 1.001084095 −0.17674663 2.39E−10 0.050990782 0 0.13957 1073. STX11 NM_003764.2 0.9255359 1.156607294 2.71E−10 5.25E−12 0 0 1074. RORA NM_002943.2 0.892828404 1.888665695 2.31E−09 3.17E−15 0 0 1075. YME1L1 NM_139313.1 0.885338942 1.012476977 7.74E−10 7.60E−11 0 0 1076. DNAJC3 NM_006260.2 0.866723986 1.604460862 1.04E−07 3.07E−12 0 0 1077. RDH5 NM_002905.2 0.86041216 −1.19985636 6.03E−09 2.00E−11 0 0 1078. DUX3 NM_012148.2 0.832695437 7.831652893 3.05E−09 1.20E−27 0 0 1079. MGC87042 XM_001128032.1 0.822066529 1.301716471 8.12E−08 3.78E−11 0 0 1080. AKIRIN1 NM_024595.1 0.817666967 1.027987047 1.72E−09 3.30E−11 0 0 1081. ACTG2 NM_001615.3 0.611516577 −1.02765041 9.24E−06 4.10E−09 3.00E−05 0 1082. OGFRL1 NM_024576.3 0.600178387 1.17123344 2.66E−05 1.39E−09 9.00E−05 0 1083. NRP1 NM_001024629.1 0.578245006 1.051207308 1.19E−06 8.05E−11 1.00E−05 0 1084. CDKN1C NM_000076.1 0.570682201 −1.05155747 1.43E−06 8.01E−11 1.00E−05 0 1085. STEAP1 NM_012449.2 0.545080861 1.029472388 1.73E−06 6.59E−11 1.00E−05 0 1086. UBE2N NM_003348.3 0.524162096 −1.07963714 4.18E−06 4.47E−11 2.00E−05 0 1087. ACO1 NM_002197.1 0.52007481 −1.15783196 4.58E−05 3.17E−10 0.00015 0 1088. CLDN5 NM_003277.2 0.502369548 −1.37078899 1.23E−05 1.26E−12 4.00E−05 0 1089. CGGBP1 NM_003663.3 0.462779712 1.045033157 4.44E−05 2.38E−10 0.00014 0 1090. LOC441455 XR_041340.1 0.441963221 1.002721498 0.000350086 5.42E−09 0.00095 0 1091. LOC651861 XM_001719902.1 0.393308176 6.597749965 0.001275915 3.94E−24 0.0031 0 1092. MCL1 NM_021960.3 0.383311489 1.672724945 0.000244946 2.57E−14 0.00068 0 1093. HNRNPAO NM_006805.3 0.345768683 −1.25021419 0.000437807 2.41E−12 0.00116 0 1094. LOC203547 NM_001017980.2 0.342264638 −1.09033514 0.001022675 1.17E−10 0.00253 0 1095. AK3L1 NM_203464.1 0.328543021 1.026597459 0.001018104 1.62E−10 0.00252 0 1096. ABL2 NM_007314.2 0.316857819 1.066692333 0.002098229 1.93E−10 0.00487 0 1097. HN1 NM_016185.2 0.307197324 −1.03615031 0.001150568 5.40E−11 0.00282 0 1098. SFRS6 NM_006275.4 0.307168529 −1.01210641 0.000906724 5.10E−11 0.00227 0 1099. HIST1H2AC NM_003512.3 0.260774576 1.066326492 0.005750248 6.64E−11 0.01218 0 1100. SOX8 NM_014587.2 0.169095918 −1.26116236 0.053417055 2.20E−12 0.09055 0 1101. ARFGEF2 NM_006420.2 0.125067472 1.336273378 0.224568998 2.47E−11 0.31242 0 1102. TIMM23B XM_928114.3 0.115549462 1.879844743 0.359592652 2.38E−12 0.45772 0 1103. LOC100133997 XM_001715556.1 0.111353621 2.784961 0.223354649 2.89E−18 0.31098 0 1104. CCL20 NM_004591.1 0.109855803 1.630861801 0.282130945 6.26E−13 0.37593 0 1105. ELK4 NM_001973.2 0.109492959 1.305687487 0.305027251 7.75E−11 0.4008 0 1106. WDR36 NM_139281.2 0.09600657 −1.06945542 0.221989934 1.06E−11 0.30948 0 1107. SPCS3 NM_021928.2 0.09520259 1.036524317 0.235186656 2.70E−11 0.32466 0 1108. ABHD2 NM_152924.3 0.091334877 1.047075939 0.388131846 3.13E−09 0.48657 0 1109. ALOX5AP NM_001629.2 0.085945199 −1.02892181 0.354225084 4.43E−10 0.45226 0 1110. FGFR4 NM_213647.1 0.082598045 −1.05368209 0.404016027 9.26E−10 0.5024 0 1111. PAFAH1B2 NM_002572.2 0.062231978 1.073521452 0.485847616 1.19E−10 0.58111 0 1112. SHD NM_020209.2 0.058233212 −1.12342048 0.486197866 1.68E−11 0.5814 0 1113. AIM2 NM_004833.1 0.038083639 1.074477056 0.775655702 9.97E−08 0.83218 0 1114. CD274 NM_014143.2 0.032275451 1.364691343 0.736102256 6.36E−12 0.79956 0 1115. FBXO6 NM_018438.4 0.031481072 1.017628884 0.740715281 9.71E−10 0.8033 0 1116. DUX2 NM_012147.2 0.030665701 1.029618827 0.716259583 9.97E−11 0.78326 0 1117. RET NM_020975.4 0.024106598 1.110768839 0.787715983 7.55E−11 0.84159 0 1118. CUL4B NM_001079872.1 0.023471479 1.098940558 0.811846314 4.88E−10 0.86066 0 1119. C10orf6 NM_018121.2 0.000177537 −1.17382939 0.998280312 6.53E−12 0.99863 0 1120. LOC652641 XM_942195.1 −0.00864993 1.077990314 0.949506215 1.35E−07 0.96253 0 1121. UBE2L3 NM_198157.1 −0.01341915 −1.09204802 0.867605419 1.57E−11 0.90231 0 1122. RALA NM_005402.2 −0.03700305 −1.21157879 0.657272573 4.40E−12 0.73323 0 1123. OLFML2B NM_015441.1 −0.04541052 −1.28414302 0.636267293 1.93E−11 0.71543 0 1124. SFRS2IP NM_004719.2 −0.05649792 −1.06811987 0.51966034 9.77E−11 0.61198 0 1125. STK17B NM_004226.2 −0.05995437 1.309143946 0.542561363 2.07E−11 0.63341 0 1126. CYP2J2 NM_000775.2 −0.06947768 1.127417514 0.504412013 7.28E−10 0.59783 0 1127. UBR1 NM_174916.1 −0.08618191 1.111143825 0.33001699 4.99E−11 0.42689 0 1128. USP13 NM_003940.2 −0.08799215 −1.03814996 0.407571152 3.90E−09 0.50579 0 1129. NES NM_006617.1 −0.08904184 −1.1178013 0.287165139 1.59E−11 0.38115 0 1130. SERPINB8 NM_198833.1 −0.10463003 1.016402892 0.277407814 9.66E−10 0.37084 0 1131. PANX1 NM_015368.3 −0.11404982 1.232833893 0.222933166 1.88E−11 0.31052 0 1132. PPM1K NM_152542.2 −0.14597856 1.440041018 0.05468873 1.39E−14 0.09244 0 1133. HSPA13 NM_006948.4 −0.17560967 1.339950446 0.066870745 4.13E−12 0.11054 0 1134. LOC649425 XM_938508.1 −0.20651231 2.538886962 0.042102553 6.55E−17 0.07337 0 1135. UHRF1 NM_001048201.1 −0.20908283 −1.03401173 0.048115314 1.91E−09 0.0826 0 1136. RUNX1 NM_001754.3 −0.21076513 −1.0466384 0.059906433 4.38E−09 0.10021 0 1137. LOC730996 XM_001128017.1 −0.2204346 1.048730809 0.012172606 3.50E−11 0.02403 0 1138. STRN NM_003162.2 −0.23478993 1.092059428 0.046030603 4.45E−09 0.07943 0 1139. AASDHPPT NM_015423.2 −0.23796404 −1.24578049 0.052732631 1.06E−09 0.08952 0 1140. SERBP1 NM_001018069.1 −0.24103121 −1.17884225 0.010692592 1.47E−11 0.02138 0 1141. SLC25A24 NM_013386.3 −0.28433847 1.103286675 0.010767317 8.54E−10 0.02152 0 1142. HIPK3 NM_005734.3 −0.29819454 1.554806445 0.006930015 1.38E−12 0.01445 0 1143. COL1A1 NM_000088.3 −0.29920476 −1.25734786 0.003454429 1.18E−11 0.00765 0 1144. ZBP1 NM_030776.1 −0.32809759 1.186552517 0.004054499 2.43E−10 0.00885 0 1145. SLC30A1 NM_021194.2 −0.34623511 1.235769639 0.00536185 5.91E−10 0.01144 0 1146. HBB NM_000518.4 −0.3539808 1.196265371 0.000443389 8.37E−12 0.00118 0 1147. REEP5 NM_005669.4 −0.35562399 −1.13758724 0.000710849 5.38E−11 0.00181 0 1148. PAFAH1B1 NM_000430.2 −0.3583053 −1.23721336 0.000353276 3.75E−12 0.00095 0 1149. GPD2 NM_001083112.1 −0.36517075 1.196546422 0.000234585 4.67E−12 0.00066 0 1150. ALPK2 NM_052947.3 −0.38259025 −1.07997593 0.000124942 2.34E−11 0.00037 0 1151. IFNB1 NM_002176.2 −0.38935446 1.043614495 0.002459152 1.24E−08 0.00563 0 1152. GPM6B NM_001001995.1 −0.3997932 −1.11868219 0.000123343 2.68E−11 0.00037 0 1153. C1orf58 NM_144695.2 −0.40749213 1.053917811 0.00094079 3.47E−09 0.00234 0 1154. CENPF NM_016343.3 −0.412248 −1.02783029 4.57E−05 4.38E−11 0.00015 0 1155. RBMS2P XR_019556.2 −0.45074102 1.313174925 0.000333757 7.03E−11 0.00091 0 1156. GMPR NM_006877.2 −0.45186814 1.360040022 0.000972186 2.83E−10 0.00242 0 1157. SLC8A1 NM_021097.2 −0.45957574 1.045939008 1.24E−05 3.33E−11 4.00E−05 0 1158. SCAMPI NM_004866.4 −0.47485584 1.368524278 1.21E−05 4.52E−13 4.00E−05 0 1159. LAMC1 NM_002293.2 −0.51077655 −1.06119464 1.71E−06 1.19E−11 1.00E−05 0 1160. SLC29A1 NM_001078174.1 −0.51113688 −1.03438508 1.87E−05 4.58E−10 7.00E−05 0 1161. RIOK3 NM_003831.2 −0.5229374 1.132954811 0.000117643 2.07E−09 0.00035 0 1162. C3orf38 NM_173824.2 −0.54578092 1.032769768 1.67E−05 1.23E−09 6.00E−05 0 1163. FGD4 NM_139241.1 −0.55922158 1.214139906 2.95E−06 1.11E−11 1.00E−05 0 1164. FEM1B NM_015322.3 −0.57078589 1.026412754 2.11E−05 3.96E−09 7.00E−05 0 1165. APOOL NM_198450.3 −0.57573228 1.369364434 1.32E−05 1.65E−11 5.00E−05 0 1166. NAMPT NM_005746.2 −0.57670041 1.209760681 2.76E−06 1.87E−11 1.00E−05 0 1167. MDM2 NM_002392.2 −0.58797092 1.078380354 7.84E−06 7.64E−10 3.00E−05 0 1168. LITAF NM_004862.2 −0.58920447 1.119550459 1.02E−05 5.89E−10 4.00E−05 0 1169. AHI1 NM_017651.3 −0.59267719 −1.05352126 9.53E−07 9.12E−11 0 0 1170. RCAN2 NM_005822.2 −0.59682376 −1.00464437 6.30E−07 1.43E−10 0 0 1171. RBMS1 NM_002897.3 −0.61592056 1.104404158 3.87E−07 2.61E−11 0 0 1172. PDGFRL NM_006207.1 −0.622703 1.202642815 8.04E−07 1.70E−11 0 0 1173. MBTPS2 NM_015884.1 −0.65389988 1.034768609 6.43E−07 4.26E−10 0 0 1174. NT5C3 NM_001002010.1 −0.6591791 1.882081623 5.40E−08 4.32E−16 0 0 1175. DCBLD1 NM_173674.1 −0.66702493 1.593519185 1.50E−07 4.36E−14 0 0 1176. OSMR NM_003999.1 −0.74169069 1.118425735 1.60E−08 1.45E−11 0 0 1177. SPPL2A NM_032802.3 −0.75238691 1.124334269 5.24E−09 4.95E−12 0 0 1178. IL4I1 NM_172374.1 −0.75714583 1.768767185 3.29E−06 3.41E−12 1.00E−05 0 1179. LOC400759 NR_003133.1 −0.76220171 1.031978608 5.83E−05 1.17E−06 0.00018 2.00E−05 1180. RBMS2 NM_002898.2 −0.77198946 1.447873733 6.48E−08 1.38E−12 0 0 1181. FAM62B NM_020728.1 −0.79375901 −1.38724639 3.35E−08 2.32E−12 0 0 1182. IL6 NM_000600.1 −0.80239057 1.19847345 7.54E−09 7.44E−12 0 0 1183. ZC3HAV1 NM_024625.3 −0.82334287 1.470989986 1.24E−07 7.17E−12 0 0 1184. ARSK NM_198150.1 −0.84351166 1.030295348 2.97E−09 9.74E−11 0 0 1185. LGALS9 NM_009587.2 −0.85488357 1.706039237 3.76E−08 2.34E−13 0 0 1186. C15orf48 NM_032413.2 −0.8681125 1.653430083 2.53E−08 3.48E−13 0 0 1187. CXCL10 NM_001565.2 −0.87657905 3.234893251 3.47E−07 3.32E−17 0 0 1188. CMPK2 NM_207315.2 −0.88262315 1.350691419 2.60E−08 1.90E−11 0 0 1189. UGCG NM_003358.1 −0.88905185 1.446532694 1.21E−09 2.09E−13 0 0 1190. GBP5 NM_052942.2 −0.90943424 1.314021934 9.28E−09 1.70E−11 0 0 1191. EEA1 NM_003566.2 −0.96299928 1.034083322 3.71E−09 1.13E−09 0 0 1192. CLIC4 NM_013943.1 −0.99759701 1.227854278 2.58E−09 7.34E−11 0 0 1193. TRIM78P NR_002777.2 −0.99905444 1.697782233 1.45E−08 1.49E−12 0 0 1194. LEPR NM_001003679.1 −1.00018695 −0.5494339 1.42E−08 6.22E−05 0 0.00055 1195. C3 NM_000064.1 −1.0004553 0.24788445 1.36E−08 0.033098399 0 0.10003 1196. ANXA1 NM_000700.1 −1.00085997 0.085372445 3.94E−11 0.279023811 0 0.47209 1197. STARD13 NM_178006.1 −1.00129109 −0.89633388 4.93E−09 2.95E−08 0 0 1198. TRIM69 NM_182985.3 −1.00157132 0.263947206 8.46E−10 0.009323484 0 0.0368 1199. TAGLN2 NM_003564.1 −1.00175678 0.054949045 6.66E−10 0.549856028 0 0.72103 1200. TIGD5 NM_032862.2 −1.00280461 −0.21629119 7.66E−10 0.027983442 0 0.08778 1201. MZF1 NM_198055.1 −1.00402759 0.055575913 8.86E−09 0.604934683 0 0.76307 1202. LOC338758 XM_931359.2 −1.00460172 −0.07165599 1.51E−10 0.398871092 0 0.59273 1203. HOXA5 NM_019102.2 −1.00487033 −0.17592457 2.05E−10 0.050905611 0 0.13942 1204. DIS3L NM_133375.2 −1.00527399 −0.27282182 1.16E−09 0.008704447 0 0.0349 1205. CKAP4 NM_006825.2 −1.00553048 0.035382271 3.69E−11 0.649924815 0 0.79516 1206. ATRIP NM_032166.2 −1.00586522 0.00213758 6.12E−11 0.978691922 0 0.99057 1207. EBPL NM_032565.2 −1.00639331 −0.09009877 2.04E−11 0.239661944 0 0.42565 1208. REC8 NM_005132.2 −1.00688308 −0.24397279 3.88E−09 0.025354659 0 0.08155 1209. PHYH NM_001037537.1 −1.00704487 −0.57574982 1.81E−10 1.33E−06 0 2.00E−05 1210. TMEM9 NM_016456.2 −1.00750993 −0.20518529 9.19E−11 0.019955494 0 0.06746 1211. CLSTN1 NM_001009566.1 −1.00859488 −0.2767763 6.84E−11 0.00246216 0 0.01224 1212. HSCB NM_172002.3 −1.00916402 0.17345123 4.20E−11 0.037214021 0 0.1096 1213. RRM2B NM_015713.3 −1.00974531 0.616053008 7.80E−11 2.56E−07 0 1.00E−05 1214. ACVRL1 NM_000020.1 −1.00990276 0.061988973 2.37E−10 0.478138188 0 0.66321 1215. SDSL NM_138432.2 −1.01062924 −0.09242636 5.14E−08 0.445803048 0 0.63538 1216. NFKB2 NM_001077493.1 −1.01108617 0.220201533 1.21E−11 0.006597758 0 0.02781 1217. ALDH2 NM_000690.2 −1.0111075 0.205252115 5.38E−10 0.033930312 0 0.10194 1218. ANTXR1 NM_053034.1 −1.01289398 0.35946479 8.37E−10 0.000948907 0 0.00552 1219. IL15 NM_000585.2 −1.01323643 −0.10288728 5.30E−11 0.20758339 0 0.38576 1220. TTC15 NM_016030.5 −1.01495273 −0.11927462 4.30E−11 0.14290549 0 0.29751 1221. ILVBL NM_006844.3 −1.01507386 −0.28026084 9.39E−11 0.002706147 0 0.01324 1222. PPM1M NM_144641.1 −1.01514806 −0.23811269 8.15E−11 0.008251188 0 0.03339 1223. ACSL1 NM_001995.2 −1.01526208 0.146999817 1.55E−08 0.199246167 0 0.37497 1224. C15orf52 NM_207380.1 −1.01586158 −0.29561857 4.88E−10 0.00375115 0 0.01746 1225. ZNF650 NM_172070.2 −1.01591905 0.690405961 1.42E−11 1.06E−08 0 0 1226. ATG7 NM_006395.1 −1.01606708 0.208256973 7.39E−09 0.063279327 0 0.1644 1227. TGFBR2 NM_001024847.1 −1.01698806 0.174313232 4.10E−10 0.06484134 0 0.16745 1228. VAMP4 NM_003762.3 −1.01752757 0.473105403 2.23E−09 0.000113827 0 0.00092 1229. BEXL1 XM_936467.2 −1.01784735 −0.15283526 2.44E−11 0.05801274 0 0.15396 1230. RUNX2 NM_001024630.2 −1.01911377 0.055237951 5.35E−11 0.495051574 0 0.67713 1231. VAMP8 NM_003761.2 −1.01962958 0.002691325 3.35E−08 0.98182034 0 0.9919 1232. LOC653583 XM_928224.2 −1.01970709 0.100451843 1.62E−10 0.249663459 0 0.43766 1233. TERF2 NM_005652.2 −1.02002113 0.331398728 1.36E−09 0.002556405 0 0.01262 1234. PTPRA NM_080841.2 −1.0200671 0.041132719 8.37E−11 0.619707912 0 0.77438 1235. TRPV2 NM_016113.3 −1.02033054 0.31160415 5.14E−10 0.002648347 0 0.01298 1236. Cxorfl2 NM_003492.1 −1.02042797 0.034624553 2.46E−09 0.73130807 0 0.84976 1237. RNF146 NM_030963.2 −1.02044138 0.146286749 6.23E−09 0.179678608 0 0.34878 1238. GAMT NM_000156.4 −1.02058409 −0.35290292 8.79E−10 0.00122572 0 0.00681 1239. GLT8D1 NM_018446.2 −1.02073656 −0.27151244 4.33E−09 0.015882461 0 0.05639 1240. WIPI1 NM_017983.4 −1.02164211 0.07989414 6.59E−11 0.33359598 0 0.53065 1241. NTN4 NM_021229.3 −1.02216955 0.03723997 2.31E−08 0.747819665 0 0.86101 1242. ZMYM3 NM_201599.1 −1.02219273 −0.01297442 3.31E−09 0.899441917 0 0.94953 1243. FAM3A NM_021806.1 −1.02234696 −0.18333266 4.83E−10 0.056482113 0 0.15086 1244. RBM23 NM_018107.4 −1.02240319 −0.07728809 8.01E−11 0.354820288 0 0.55116 1245. SMARCD3 NM_003078.3 −1.02245569 −0.3421277 3.73E−11 0.000300327 0 0.00209 1246. C1orf131 NM_152379.2 −1.02288052 −0.08788694 4.23E−10 0.3396059 0 0.5365 1247. RNF213 NM_020914.3 −1.02352275 0.630793255 3.71E−10 8.21E−07 0 2.00E−05 1248. DNAJB4 NM_007034.3 −1.02382303 0.413005013 4.52E−08 0.002525128 0 0.01248 1249. ULBP1 NM_025218.2 −1.02464222 0.619275117 1.00E−08 1.52E−05 0 0.00017 1250. IDS NM_000202.3 −1.02471053 0.665503463 1.20E−10 1.44E−07 0 0 1251. SLC16A5 NM_004695.2 −1.02541031 −0.03968265 3.36E−09 0.70079185 0 0.82953 1252. TINF2 NM_012461.1 −1.02546681 0.386138648 3.63E−10 0.000339715 0 0.00232 1253. GAS6 NM_000820.1 −1.02587109 −0.31870511 4.47E−11 0.000683668 0 0.0042 1254. SLC43A3 NM_017611.2 −1.02596127 0.437566237 1.02E−09 0.000175557 0 0.00132 1255. FAM156A NM_014138.3 −1.02743694 −0.13647211 1.98E−10 0.129889659 0 0.27791 1256. ASAP2 NM_003887.2 −1.02803205 −0.34231267 2.73E−11 0.000263984 0 0.00188 1257. GJD3 NM_152219.3 −1.02847929 0.864574016 1.35E−10 2.62E−09 0 0 1258. C2orf28 NM_080592.2 −1.02874375 −0.07858913 4.95E−11 0.33696391 0 0.53401 1259. EFEMP1 NM_001039348.1 −1.02978102 −0.20772504 1.74E−10 0.025432771 0 0.08174 1260. GSTO1 NM_004832.1 −1.03007833 0.314163517 4.61E−11 0.000823775 0 0.00491 1261. D2HGDH NM_152783.3 −1.03061752 −0.3981992 3.73E−09 0.000983544 0 0.00569 1262. PTEN NM_000314.4 −1.03096663 −0.30285484 2.76E−11 0.000890422 0 0.00524 1263. RAB13 NM_002870.2 −1.03194193 0.349571805 5.53E−09 0.003547841 0 0.01664 1264. APBA3 NM_004886.3 −1.03241529 0.001776099 1.06E−11 0.980961543 0 0.9915 1265. MGST1 NM_145792.1 −1.03246386 0.227081996 6.67E−11 0.011534287 0 0.04357 1266. MGLL NM_007283.5 −1.0334287 −0.00330488 4.32E−11 0.967298433 0 0.98544 1267. MOSC1 NM_022746.2 −1.03390536 −0.10838932 6.41E−08 0.389841994 0 0.58474 1268. ZNF672 NM_024836.1 −1.03400454 −0.14813865 8.74E−10 0.133783769 0 0.28365 1269. CDC42EP4 NM_012121.4 −1.03422592 0.066327892 5.16E−11 0.419663147 0 0.61177 1270. NUDT18 NM_024815.3 −1.03435449 0.169208751 2.09E−10 0.066744183 0 0.17107 1271. MXD4 NM_006454.2 −1.03509964 −0.91679597 5.02E−09 3.56E−08 0 0 1272. TMEM189-UBE2V1 NM_199203.1 −1.03579522 0.063781062 7.55E−10 0.505651759 0 0.68575 1273. SLC9A3R1 NM_004252.2 −1.03608282 −0.06339429 5.02E−11 0.440271783 0 0.63064 1274. DENND5A NM_015213.2 −1.03650108 0.079913603 8.79E−12 0.28696254 0 0.48133 1275. HOXB7 NM_004502.3 −1.03685924 −0.06123515 4.39E−11 0.45275097 0 0.64195 1276. PACSIN2 NM_007229.1 −1.03777942 −0.32531045 3.09E−11 0.000515457 0 0.00331 1277. ACCS NM_032592.3 −1.03842113 −0.15573423 1.20E−10 0.081305814 0 0.19845 1278. XPO1 NM_003400.3 −1.03964261 −0.23248685 3.98E−10 0.018989932 0 0.06495 1279. C20orf72 NM_052865.2 −1.03987237 −0.05253853 5.69E−11 0.525881169 0 0.70174 1280. ITGA3 NM_002204.1 −1.04102345 0.126786496 6.97E−11 0.139776672 0 0.29239 1281. IRF2BP2 NM_182972.2 −1.04105083 −0.80601308 1.76E−10 1.30E−08 0 0 1282. SRC NM_198291.1 −1.04134599 0.056904895 3.78E−11 0.483095417 0 0.6673 1283. LOC285296 XM_001714301.1 −1.04185053 0.824626417 6.62E−11 3.62E−09 0 0 1284. MYF6 NM_002469.1 −1.04218609 −0.02360164 3.67E−10 0.797483378 0 0.89132 1285. ZFP36 NM_003407.2 −1.04372218 0.231703522 7.05E−11 0.011107992 0 0.04224 1286. C4orf34 NM_174921.1 −1.04434188 0.611877122 5.29E−12 4.71E−08 0 0 1287. FAM57A NM_024792.1 −1.04479032 −0.00313515 9.16E−10 0.9742696 0 0.98794 1288. LSS NM_002340.3 −1.04498765 −0.00730124 9.00E−11 0.931544337 0 0.96702 1289. MME NM_000902.3 −1.04587432 −0.18403688 7.15E−11 0.038349759 0 0.11221 1290. SULF2 NM_018837.2 −1.04795874 −0.04816615 3.65E−11 0.553792099 0 0.72451 1291. ATP6AP1L NM_001017971.1 −1.04946395 0.02802534 7.28E−11 0.739990972 0 0.85518 1292. RCOR2 NM_173587.2 −1.05065782 −0.19485673 1.98E−09 0.068327822 0 0.1741 1293. FAM160B1 NM_020940.3 −1.05090412 0.628169983 3.44E−10 1.19E−06 0 2.00E−05 1294. RFX5 NM_001025603.1 −1.05207078 −0.06022618 1.38E−11 0.43746356 0 0.62822 1295. FAM65A NM_024519.2 −1.05253845 −0.12629991 1.27E−10 0.15875063 0 0.32029 1296. TRIM55 NM_184086.1 −1.05288688 0.196695804 1.84E−11 0.019444539 0 0.06604 1297. MYPOP NM_001012643.2 −1.05317044 −0.03552199 2.19E−11 0.654134469 0 0.79802 1298. TCFL5 NM_006602.2 −1.05337852 0.033604893 3.48E−12 0.638799111 0 0.78755 1299. GPR1 NM_001098199.1 −1.05391401 0.220118451 3.83E−11 0.01303422 0 0.04819 1300. IGDCC4 NM_020962.1 −1.05413923 −0.52159292 2.30E−11 1.94E−06 0 3.00E−05 1301. ARHGEF2 NM_004723.2 −1.05674634 −0.07135827 6.16E−11 0.400540634 0 0.59451 1302. CCND2 NM_001759.2 −1.05683056 −0.52817599 1.20E−09 3.25E−05 0 0.00032 1303. EEF2K NM_013302.3 −1.05774489 −0.53218489 1.24E−11 9.44E−07 0 2.00E−05 1304. CASP4 NM_001225.3 −1.05930929 0.690796965 4.20E−11 5.41E−08 0 0 1305. RNASE4 NM_194431.1 −1.06008853 −0.1107261 2.08E−10 0.2296911 0 0.41321 1306. AUH NM_001698.1 −1.06019572 0.160413368 2.35E−11 0.05577631 0 0.14961 1307. TDRD7 NM_014290.1 −1.06193552 1.072280332 1.18E−09 1.01E−09 0 0 1308. RCN3 NM_020650.2 −1.06243068 −0.20210498 2.00E−11 0.01808814 0 0.06246 1309. JUNB NM_002229.2 −1.06337011 0.515245722 1.65E−10 1.14E−05 0 0.00013 1310. HAS1 NM_001523.1 −1.06338584 0.217026478 5.25E−09 0.059345921 0 0.1566 1311. C14orf93 NM_021944.1 −1.06340255 −0.10731526 3.28E−11 0.198485007 0 0.37388 1312. PPP2R2C NM_181876.2 −1.06387129 −0.23080346 6.30E−10 0.025665245 0 0.08234 1313. ANGPTL4 NM_139314.1 −1.06440002 1.266897552 1.39E−09 6.94E−11 0 0 1314. FXYD5 NM_144779.1 −1.06511972 0.094610302 3.23E−11 0.255044755 0 0.4434 1315. HOM-TES-103 NM_080731.1 −1.06515635 −0.31655432 1.51E−10 0.001860683 0 0.0097 1316. FLT3LG NM_001459.2 −1.0654256 0.38728166 5.98E−11 0.000167558 0 0.00127 1317. GBA NM_001005742.1 −1.06545864 0.288978323 2.35E−11 0.001652062 0 0.00878 1318. ETS1 NM_005238.2 −1.06666678 −0.1783118 8.53E−09 0.127470143 0 0.2745 1319. THY1 NM_006288.2 −1.06677074 −0.64440098 1.24E−11 6.13E−08 0 0 1320. AARS NM_001605.2 −1.06728577 0.277572737 6.67E−11 0.003689333 0 0.01725 1321. NDST1 NM_001543.3 −1.06902065 −0.69119706 1.51E−09 1.34E−06 0 2.00E−05 1322. ALOX15B NM_001141.2 −1.07066744 0.451755678 9.89E−10 0.000192752 0 0.00143 1323. TAX1BP3 NM_014604.2 −1.07230743 −0.34095702 6.77E−11 0.000685354 0 0.0042 1324. RILPL1 NM_178314.2 −1.0723764 0.623268364 5.01E−10 2.40E−06 0 4.00E−05 1325. FEZ1 NM_022549.2 −1.07316721 0.189981814 5.49E−11 0.03482 0 0.10397 1326. KTELC1 NM_020231.3 −1.07325158 0.156414048 8.86E−12 0.052061477 0 0.14186 1327. RHOT1 NM_001033566.1 −1.07434479 0.330750314 3.74E−12 0.000188365 0 0.0014 1328. MAP3K6 NM_004672.3 −1.07445986 −0.22682833 3.93E−11 0.012330138 0 0.04603 1329. TBC1D2 NM_018421.2 −1.07454756 0.292616438 6.85E−10 0.006929103 0 0.02898 1330. FAM189B NM_006589.2 −1.07523534 0.040193947 1.48E−10 0.655893355 0 0.79969 1331. NUP37 NM_024057.2 −1.075314 −0.13391316 1.11E−11 0.096579133 0 0.22414 1332. PSAT1 NM_021154.3 −1.07567406 0.736451787 3.35E−11 2.05E−08 0 0 1333. PLEKHA2 NM_021623.1 −1.07712827 0.062003171 4.81E−11 0.466371544 0 0.65369 1334. BID NM_197966.1 −1.07811035 −0.16745726 8.96E−12 0.039744067 0 0.11553 1335. HS1BP3 NM_022460.3 −1.07839537 0.051425836 2.84E−11 0.533427888 0 0.70789 1336. ARSD NM_001669.2 −1.07860998 −0.20520685 1.08E−10 0.029680584 0 0.09185 1337. GSTK1 NM_015917.1 −1.07866338 0.059298016 4.51E−12 0.427729021 0 0.61948 1338. ACPL2 NM_152282.3 −1.07921904 0.14679038 6.29E−11 0.099555678 0 0.22935 1339. RNF31 NM_017999.4 −1.07984343 0.051415213 1.87E−10 0.576016056 0 0.74068 1340. TBK1 NM_013254.2 −1.08002803 0.357183055 3.94E−11 0.000348733 0 0.00237 1341. NOTCH1 NM_017617.3 −1.08006 −0.66953259 2.93E−09 4.13E−06 0 6.00E−05 1342. C20orf117 NM_199181.2 −1.08011362 −0.53217661 2.09E−11 1.91E−06 0 3.00E−05 1343. HLA-A NM_002116.5 −1.08013352 0.557697842 1.59E−08 0.000134164 0 0.00105 1344. CYFIP2 NM_001037333.1 −1.08099479 −0.63302219 2.29E−11 1.67E−07 0 0 1345. ATP2B1 NM_001001323.1 −1.0817218 −0.70390831 4.82E−09 3.21E−06 0 5.00E−05 1346. ZKSCAN1 NM_003439.1 −1.0817446 0.380240593 1.65E−08 0.004447165 0 0.0201 1347. C8orf55 NM_016647.2 −1.0823364 −0.38704721 3.80E−11 0.000151713 0 0.00117 1348. CLIC1 NM_001288.4 −1.08331855 0.308893162 6.15E−12 0.000538018 0 0.00343 1349. ARHGAP22 NM_021226.2 −1.08424685 0.077731251 2.72E−11 0.351028366 0 0.54746 1350. NADSYN1 NM_018161.4 −1.08625609 0.118208324 2.30E−11 0.158998903 0 0.32067 1351. DRAM1 NM_018370.2 −1.08687246 −0.36488141 4.65E−11 0.000329433 0 0.00226 1352. SHMT2 NM_005412.4 −1.08862162 0.261511532 1.09E−10 0.00787209 0 0.03216 1353. PTGFR NM_000959.3 −1.08884041 0.149623299 2.17E−10 0.119685358 0 0.26244 1354. CXCL16 NM_022059.1 −1.09023442 1.183509176 9.24E−11 2.17E−11 0 0 1355. CD68 NM_001251.1 −1.0912592 1.175059517 3.43E−10 9.47E−11 0 0 1356. NRSN2 NM_024958.1 −1.09142027 0.068072359 2.96E−12 0.358447094 0 0.55456 1357. LOC730278 XM_001126471.1 −1.09182645 0.189911348 7.13E−10 0.069266329 0 0.176 1358. THBS1 NM_003246.2 −1.09190365 −0.56593524 4.24E−11 1.64E−06 0 3.00E−05 1359. NFE2L2 NM_006164.2 −1.09267987 0.32900533 9.58E−12 0.000402512 0 0.00268 1360. LOC728060 XR_015272.2 −1.09472957 0.25532926 8.89E−11 0.008837118 0 0.03525 1361. AP1S1 NM_057089.2 −1.09532783 −0.14035425 8.83E−10 0.177712026 0 0.3462 1362. CAV1 NM_001753.3 −1.09664018 −0.19112993 4.09E−11 0.03465702 0 0.10359 1363. BEX1 NM_018476.3 −1.09691667 −0.23461683 4.30E−11 0.011748596 0 0.04419 1364. PRKD1 NM_002742.2 −1.09863799 −0.6085326 4.20E−11 6.33E−07 0 1.00E−05 1365. WEE1 NM_003390.2 −1.09868601 0.332519669 3.81E−10 0.002478081 0 0.0123 1366. PRKAG2 NM_024429.1 −1.09879065 0.754723456 6.53E−12 4.39E−09 0 0 1367. HCP5 NM_006674.2 −1.09901267 0.144295449 1.82E−11 0.088959444 0 0.21176 1368. SLC24A6 NM_024959.2 −1.09932642 0.00010176 8.15E−10 0.999200656 0 0.9996 1369. C2orf32 NM_015463.1 −1.09974886 0.078131125 1.18E−10 0.394204315 0 0.58867 1370. DPYSL2 NM_001386.4 −1.09989485 0.228537719 1.59E−11 0.009925877 0 0.03863 1371. ETV6 NM_001987.4 −1.1000486 −0.0553284 1.19E−10 0.544679472 0 0.71702 1372. ODF3B NM_001014440.2 −1.10039204 0.42956235 1.46E−11 3.03E−05 0 3.00E−04 1373. PEX16 NM_004813.1 −1.10070279 0.024268324 5.42E−10 0.8070527 0 0.89681 1374. SH3PXD2B NM_001017995.1 −1.10111105 −0.01555465 9.36E−12 0.843659438 0 0.91755 1375. BEST1 NM_004183.2 −1.1014659 0.266093011 1.05E−11 0.00292983 0 0.01419 1376. LRP10 NM_014045.3 −1.10241025 0.415789662 7.02E−12 2.80E−05 0 0.00028 1377. PMP22 NM_153321.1 −1.10263074 0.266687734 1.39E−10 0.008249178 0 0.03339 1378. RIPK1 NM_003804.3 −1.10270158 −0.24065996 1.05E−09 0.028965073 0 0.09019 1379. WNT5A NM_003392.3 −1.10285871 −0.39934446 4.58E−10 0.000568039 0 0.00359 1380. LOC390530 XM_372543.2 −1.10354111 0.10829986 1.40E−09 0.310194598 0 0.5057 1381. TXNRD2 NM_006440.3 −1.10446667 −0.16661747 1.31E−10 0.081135275 0 0.19814 1382. ENG NM_000118.1 −1.1045979 0.492655113 2.40E−10 4.11E−05 0 0.00039 1383. MOBKL2C NM_145279.4 −1.10570526 0.127380024 1.17E−09 0.231058038 0 0.41488 1384. PPAP2A NM_176895.1 −1.10579812 0.544950169 3.75E−12 4.86E−07 0 1.00E−05 1385. PFKP NM_002627.3 −1.10605138 0.775927102 2.83E−10 9.46E−08 0 0 1386. HOXC13 NM_017410.2 −1.1072319 0.443969061 7.06E−11 6.28E−05 0 0.00056 1387. IL10RB NM_000628.3 −1.1077727 −0.05056423 5.67E−12 0.514424403 0 0.69225 1388. APOBEC3C NM_014508.2 −1.10809902 0.58273362 2.15E−10 4.77E−06 0 7.00E−05 1389. FES NM_002005.2 −1.1084545 −0.33138799 2.07E−09 0.00572525 0 0.02471 1390. P4HB NM_000918.3 −1.10933616 −0.19271039 3.57E−11 0.033945125 0 0.10198 1391. HLA-E NM_005516.4 −1.11004281 0.814748655 4.85E−11 9.34E−09 0 0 1392. BCL9L NM_182557.2 −1.11143745 0.732633231 3.58E−09 2.11E−06 0 3.00E−05 1393. ZBTB25 NM_006977.2 −1.11264019 0.346301575 6.27E−12 0.000226809 0 0.00165 1394. FAM156B NM_001099684.1 −1.11275453 −0.17123139 2.46E−11 0.052634938 0 0.14315 1395. SPG7 NM_003119.2 −1.11281034 −0.27955345 1.99E−10 0.007357358 0 0.03043 1396. MYOD1 NM_002478.4 −1.11297689 −0.46196618 5.42E−11 3.51E−05 0 0.00034 1397. NPEPL1 NM_024663.3 −1.11311504 −0.2630971 1.91E−10 0.010720106 0 0.041 1398. OPTN NM_001008213.1 −1.1134359 −0.572683 4.48E−12 2.99E−07 0 1.00E−05 1399. TRIM5 NM_033034.1 −1.11392597 0.500305535 7.09E−11 1.61E−05 0 0.00018 1400. GRAMD3 NM_023927.1 −1.11531797 0.377216655 8.33E−11 0.000425196 0 0.00281 1401. RFNG XM_001132711.1 −1.11554495 −0.21827894 8.64E−12 0.011678522 0 0.04397 1402. PDE7B NM_018945.3 −1.11590806 −0.56949559 2.06E−10 6.86E−06 0 9.00E−05 1403. ARMCX1 NM_016608.1 −1.11598479 −0.06031382 1.88E−10 0.526265431 0 0.70214 1404. FRMD3 NM_174938.3 −1.11602118 −0.29070138 1.81E−12 0.000667962 0 0.00412 1405. C1orf57 NM_032324.1 −1.11721778 0.354382035 2.69E−11 0.000425597 0 0.00281 1406. PRMT2 NM_001535.2 −1.11885544 0.074119142 5.94E−11 0.408451827 0 0.60212 1407. ZNF319 NM_020807.1 −1.11891714 −0.08178541 8.56E−12 0.31132616 0 0.50689 1408. SLC2A10 NM_030777.3 −1.11896209 −0.31968771 2.99E−11 0.00118681 0 0.00663 1409. CDR2L NM_014603.1 −1.11911242 −0.20301163 1.21E−12 0.009511858 0 0.03735 1410. CORO6 NM_032854.2 −1.12027819 −0.3003946 6.27E−10 0.007421803 0 0.03065 1411. LBA1 NM_014831.1 −1.12086965 0.495819259 5.43E−10 7.83E−05 0 0.00067 1412. CERCAM NM_016174.3 −1.12092245 −0.18379352 8.87E−11 0.054639249 0 0.14726 1413. CTDSP1 NM_021198.1 −1.12174762 0.041546061 3.63E−11 0.632601165 0 0.78317 1414. PCBP3 NM_020528.1 −1.12178489 0.211347399 3.76E−10 0.04325855 0 0.12317 1415. TIAF1 NM_004740.3 −1.12263209 −0.52935476 1.55E−11 2.78E−06 0 4.00E−05 1416. LPXN NM_004811.1 −1.12383405 −0.01760094 2.14E−11 0.834629425 0 0.91265 1417. TYMS NM_001071.1 −1.1252785 −0.09199154 7.27E−12 0.254866653 0 0.4433 1418. FKBP11 NM_016594.1 −1.12528495 0.300590026 1.63E−11 0.001581497 0 0.00846 1419. PSRC1 NM_001032290.1 −1.12569454 −0.48705968 1.13E−10 3.52E−05 0 0.00034 1420. FAM129B NM_022833.2 −1.12586668 0.438215519 1.32E−11 2.93E−05 0 3.00E−04 1421. LUM NM_002345.3 −1.12592585 0.386922869 5.27E−11 0.000279368 0 0.00197 1422. LYRM1 NM_020424.2 −1.12605499 0.014914193 8.10E−13 0.832436921 0 0.91152 1423. TNFRSF10A NM_003844.2 −1.12617958 0.844102309 1.25E−10 1.59E−08 0 0 1424. ACP2 NM_001610.1 −1.12624234 0.222500267 2.14E−10 0.02992589 0 0.09239 1425. SYNC1 NM_030786.1 −1.12665499 −0.25080558 3.63E−09 0.037412442 0 0.11009 1426. USP41 XM_036729.5 −1.12677811 0.524575184 2.23E−11 4.34E−06 0 6.00E−05 1427. TNFSF10 NM_003810.2 −1.12685752 2.971672323 3.25E−08 1.06E−15 0 0 1428. LOC645638 XR_040455.1 −1.12764118 −0.07112827 1.14E−11 0.388206869 0 0.58348 1429. PID1 NM_017933.3 −1.12788845 0.314029719 1.09E−11 0.000903744 0 0.00531 1430. TOM1 NM_005488.1 −1.12875228 4.81E−05 6.50E−12 0.999515526 0 0.99971 1431. GBE1 NM_000158.2 −1.12885253 0.481765414 3.55E−12 3.53E−06 0 5.00E−05 1432. PNPO NM_018129.2 −1.13041513 −0.02587896 1.55E−11 0.756193528 0 0.86627 1433. LHFPL2 NM_005779.1 −1.13042882 −0.14372411 3.01E−09 0.212228234 0 0.39165 1434. CST3 NM_000099.2 −1.13121662 0.157381243 8.62E−12 0.062234167 0 0.16234 1435. SLC44A1 NM_080546.3 −1.13216786 0.780099421 7.54E−12 4.76E−09 0 0 1436. SLC35E3 NM_018656.2 −1.13240472 0.461873605 8.16E−11 5.67E−05 0 0.00051 1437. RXRA NM_002957.3 −1.13242382 −0.32017726 3.82E−12 0.00045236 0 0.00296 1438. CREB1 NM_004379.2 −1.13307916 −0.08534387 2.95E−12 0.269699958 0 0.46109 1439. FAS NM_152877.1 −1.13338054 0.145223093 6.87E−11 0.121108539 0 0.26477 1440. SLC22A4 NM_003059.2 −1.13425744 0.381696472 2.78E−10 0.000858012 0 0.00508 1441. NOD2 NM_022162.1 −1.13496736 0.434713135 2.09E−11 4.81E−05 0 0.00045 1442. ASB5 NM_080874.2 −1.13535655 −0.4567075 2.29E−11 2.85E−05 0 0.00029 1443. IFI27L2 NM_032036.2 −1.13681021 −0.02949474 7.49E−10 0.778016481 0 0.87915 1444. CDC42EP5 NM_145057.2 −1.13701196 0.138705526 6.69E−10 0.191469223 0 0.36534 1445. TP53INP1 NM_033285.2 −1.13775234 −0.57336685 1.81E−10 7.33E−06 0 9.00E−05 1446. PSME1 NM_006263.2 −1.13780064 0.277504124 1.77E−12 0.001200584 0 0.00669 1447. FAT1 NM_005245.3 −1.13818248 0.40548035 1.04E−10 0.000286767 0 0.00201 1448. CRTC3 NM_022769.3 −1.13844672 −0.1184239 1.30E−11 0.164245027 0 0.32791 1449. LOC650215 XR_018889.1 −1.13895881 0.63860381 1.45E−12 3.07E−08 0 0 1450. EMP3 NM_001425.1 −1.13943282 −0.2096233 4.38E−11 0.027188079 0 0.0858 1451. TRIM56 NM_030961.1 −1.13956107 0.308557613 2.89E−11 0.001845441 0 0.00964 1452. LOC728809 XM_001719546.1 −1.14043153 0.022132969 8.26E−11 0.810618999 0 0.89891 1453. C11orf68 NM_031450.2 −1.14152841 0.36162395 1.71E−11 0.000335143 0 0.0023 1454. PEX11B NM_003846.1 −1.14215923 −0.22122472 7.10E−11 0.024066538 0 0.07834 1455. PDE4B NM_002600.3 −1.14298689 0.675737387 1.50E−11 1.01E−07 0 0 1456. LOC653506 XM_927769.1 −1.1440126 0.017475514 1.03E−11 0.832048635 0 0.91125 1457. CBLN3 NM_001039771.2 −1.14406425 0.154256286 7.01E−11 0.104314005 0 0.23731 1458. OSBPL7 NM_145798.2 −1.14474535 −0.36688245 2.21E−11 0.000344523 0 0.00235 1459. HIF1A NM_181054.1 −1.14976405 0.420889531 1.73E−07 0.009415561 0 0.0371 1460. MFGE8 NM_005928.1 −1.14980935 0.032536086 1.42E−11 0.699932682 0 0.829 1461. LASP1 NM_006148.1 −1.15156327 −0.45518784 5.84E−11 6.54E−05 0 0.00058 1462. ATP6V0A1 NM_005177.3 −1.15218372 −0.04496838 1.54E−11 0.597306092 0 0.75747 1463. KCNK2 NM_001017425.2 −1.15404288 0.213670594 5.89E−12 0.014302853 0 0.05175 1464. ZC3H5 XM_940903.2 −1.15463553 0.096519659 1.10E−10 0.31594441 0 0.51185 1465. LTBR NM_002342.1 −1.15479546 0.406067224 3.19E−11 0.000163502 0 0.00125 1466. TXLNA NM_175852.3 −1.15663244 −0.16212822 3.89E−11 0.082358746 0 0.20036 1467. SMARCAL1 NM_014140.2 −1.15668354 0.016691468 5.28E−11 0.854947241 0 0.92393 1468. TOP2A NM_001067.2 −1.15703548 −0.60645497 5.01E−11 1.60E−06 0 3.00E−05 1469. IRS1 NM_005544.1 −1.15737634 0.275274975 3.14E−12 0.001939901 0 0.01004 1470. SLC44A2 NM_020428.2 −1.15807453 −0.34567202 1.15E−11 0.000484719 0 0.00315 1471. CYP4V2 NM_207352.2 −1.15927998 −0.49894739 2.01E−11 1.12E−05 0 0.00013 1472. MTSS1 NM_014751.4 −1.15938641 −0.4144808 7.77E−10 0.00085324 0 0.00506 1473. LOC100129165 XM_001718314.1 −1.160536 0.22453105 6.53E−12 0.011377742 0 0.04309 1474. PARD6G NM_032510.3 −1.16124563 −0.01048755 1.51E−09 0.924905714 0 0.96364 1475. KDELR3 NM_006855.2 −1.16287967 −0.44400682 1.25E−11 3.55E−05 0 0.00035 1476. ADAMTS1 NM_006988.3 −1.16353852 0.176486006 4.09E−10 0.099095848 0 0.22859 1477. ZNF302 NM_018443.2 −1.16400043 −0.01005428 9.96E−11 0.915918023 0 0.95951 1478. PSPH NM_004577.3 −1.16402902 0.005653554 1.18E−11 0.946619231 0 0.97406 1479. FRMD4A NM_018027.3 −1.16430189 −0.54533485 2.39E−12 7.09E−07 0 1.00E−05 1480. LOC644739 XM_933679.1 −1.16529261 −0.07398917 1.32E−11 0.388790686 0 0.58399 1481. ZMIZ1 NM_020338.2 −1.16533295 −0.03786985 1.58E−11 0.660091727 0 0.80268 1482. NPR2 NM_003995.3 −1.16612668 −0.04505504 7.81E−11 0.633005094 0 0.78323 1483. ID1 NM_181353.1 −1.16641588 0.732925025 2.20E−10 3.99E−07 0 1.00E−05 1484. NLRX1 NM_170722.1 −1.16689384 −0.14091168 1.48E−11 0.111746507 0 0.24973 1485. C14orf173 NM_022489.2 −1.16706082 −0.27135286 1.26E−12 0.001543132 0 0.00828 1486. HECW2 NM_020760.1 −1.16735475 0.06016212 4.75E−12 0.458021473 0 0.64645 1487. RAB40C NM_021168.2 −1.16811719 −0.07137997 5.03E−10 0.498862564 0 0.68032 1488. UGP2 NM_006759.3 −1.16853639 0.1108138 2.32E−11 0.217100893 0 0.39777 1489. CASP1 NM_033294.2 −1.1695189 2.170829048 9.36E−11 1.09E−15 0 0 1490. CPSF4 NM_001081559.1 −1.17121049 −0.26735466 2.30E−12 0.002357768 0 0.01182 1491. HIPK2 NM_022740.2 −1.1726493 0.355894491 1.36E−11 0.000451829 0 0.00296 1492. MTHFD1L NM_015440.3 −1.17347948 0.395510823 2.09E−09 0.002336701 0 0.01173 1493. ABLIM3 NM_014945.2 −1.17381801 0.014951687 6.43E−11 0.873205983 0 0.93426 1494. CDH11 NM_001797.2 −1.17432107 0.241948208 7.01E−11 0.017195516 0 0.05996 1495. TSPAN4 NM_001025235.1 −1.17498403 −0.1168688 1.70E−11 0.188981063 0 0.36212 1496. JSRP1 NM_144616.2 −1.17536966 −0.46610287 4.52E−11 5.33E−05 0 0.00049 1497. FBXO32 NM_058229.2 −1.17650838 0.766554709 7.49E−11 9.12E−08 0 0 1498. NCOR2 NM_001077261.1 −1.17671645 −0.22413702 1.11E−10 0.029713388 0 0.09193 1499. MVP NM_005115.3 −1.17773371 −0.11621563 2.34E−10 0.258710293 0 0.44815 1500. RAB7L1 NM_003929.1 −1.17839739 0.431475634 3.43E−11 0.000110172 0 0.00089 1501. PLOD1 NM_000302.2 −1.178952 −0.14685537 9.83E−12 0.094426723 0 0.22099 1502. PDE4C NM_000923.2 −1.1793672 0.39519008 2.51E−11 0.000235677 0 0.00171 1503. HEG1 NM_020733.1 −1.17979515 −0.25402563 6.03E−12 0.005461985 0 0.02376 1504. MT1F NM_005949.2 −1.18264076 −0.54040845 9.47E−12 2.92E−06 0 4.00E−05 1505. CREB3L2 NM_194071.2 −1.1832544 −0.24768779 9.38E−12 0.007830541 0 0.03203 1506. CAPN5 NM_004055.4 −1.18408225 −0.54314396 4.66E−10 4.65E−05 0 0.00043 1507. ABCB6 NM_005689.1 −1.18409135 −0.26892257 9.07E−12 0.004383415 0 0.01986 1508. SYT7 NM_004200.2 −1.18426444 −0.64787893 7.44E−10 7.35E−06 0 9.00E−05 1509. PTGER2 NM_000956.2 −1.18447658 −0.20234692 6.06E−12 0.022534326 0 0.07414 1510. BCAR3 NM_003567.2 −1.18488673 −0.14847184 9.33E−12 0.091752592 0 0.21651 1511. SMYD4 NM_052928.1 −1.18510331 0.20769913 1.41E−11 0.025163935 0 0.08104 1512. TRIM8 NM_030912.2 −1.18538697 −0.35362965 8.85E−12 0.000422075 0 0.0028 1513. ZMYM6 NM_007167.2 −1.18603894 −0.0076299 1.93E−12 0.921888653 0 0.96232 1514. PLEKHF1 NM_024310.4 −1.18680825 0.197467933 9.92E−10 0.086780708 0 0.20818 1515. TMED10P NR_002807.1 −1.18683315 0.445570742 9.38E−12 3.59E−05 0 0.00035 1516. FAM174B NM_207446.2 −1.18772948 −0.57106759 2.04E−11 2.62E−06 0 4.00E−05 1517. C1S NM_201442.1 −1.18845168 0.420876179 2.47E−11 0.000129486 0 0.00102 1518. LOC728855 NR_024510.1 −1.18875133 0.424067129 8.83E−11 0.000257397 0 0.00184 1519. NEXN NM_144573.3 −1.18929137 −0.26453691 3.65E−11 0.008666296 0 0.03478 1520. STC2 NM_003714.2 −1.18948843 −0.36095397 4.80E−11 0.000880696 0 0.00519 1521. AMZ2 NM_001033569.1 −1.19097704 0.016471304 7.00E−12 0.844432069 0 0.91796 1522. CAV2 NM_001233.3 −1.19188498 0.426664771 1.65E−12 1.99E−05 0 0.00021 1523. SLC9A1 NM_003047.2 −1.19305498 0.199296174 1.81E−11 0.034100478 0 0.10232 1524. FYN NM_153047.1 −1.19385877 0.309464943 2.32E−10 0.006309822 0 0.02678 1525. POLR3GL NM_032305.1 −1.19407945 −0.09916688 2.93E−12 0.224900502 0 0.40707 1526. LOC374395 NM_199337.1 −1.19589143 0.359938265 5.26E−13 7.44E−05 0 0.00065 1527. IKBKE NM_014002.2 −1.19669054 0.392291897 1.19E−10 0.000695024 0 0.00425 1528. TMEM62 NM_024956.3 −1.19734084 1.21981219 6.64E−11 4.79E−11 0 0 1529. C1orf66 NM_015997.2 −1.19808133 −0.08346608 5.82E−12 0.323871883 0 0.52047 1530. SPG21 NM_016630.3 −1.19894761 −0.00716397 6.00E−12 0.931828283 0 0.96715 1531. C7orf10 NM_024728.1 −1.20046313 −0.317807 7.86E−13 0.000368054 0 0.00249 1532. CFD NM_001928.2 −1.20124234 0.252196355 1.59E−11 0.009307691 0 0.03675 1533. SAMD4A NM_015589.3 −1.20155458 1.120292909 4.96E−10 1.63E−09 0 0 1534. APOBEC3F NM_001006666.1 −1.2031046 0.59819306 7.76E−11 4.62E−06 0 6.00E−05 1535. SIDT2 NM_001040455.1 −1.20512141 −0.30213165 7.56E−13 0.000611251 0 0.00382 1536. PHF21A NM_016621.2 −1.20733303 0.058049641 9.48E−13 0.449476415 0 0.63891 1537. RPS6KA2 NM_001006932.1 −1.20796669 −0.37413204 9.28E−13 7.63E−05 0 0.00066 1538. RRAS2 NM_012250.3 −1.21247895 0.410022176 3.59E−12 6.54E−05 0 0.00058 1539. ABCA1 NM_005502.2 −1.21273165 −0.32058912 2.86E−11 0.002235251 0 0.01131 1540. ASPSCR1 NM_024083.2 −1.21390751 −0.30717198 4.40E−12 0.001346061 0 0.00737 1541. SLC39A8 NM_022154.5 −1.21704059 0.899188177 1.04E−08 1.05E−06 0 2.00E−05 1542. BLOC1S2 NM_001001342.1 −1.21927547 0.446363395 1.59E−11 6.80E−05 0 6.00E−04 1543. C7orf68 NM_013332.3 −1.22027849 0.31970722 1.22E−11 0.001623931 0 0.00866 1544. IFNGR2 NM_005534.2 −1.22112757 0.022584497 1.33E−12 0.773769074 0 0.87642 1545. SAA2 NM_030754.2 −1.22134171 0.281324169 6.74E−09 0.037996565 0 0.11141 1546. LOC642567 XR_038054.1 −1.22197896 0.561394485 6.83E−08 0.001055478 0 0.00603 1547. SPG11 NM_025137.3 −1.22356765 0.295100761 3.20E−12 0.001743243 0 0.00918 1548. ALDH3B1 NM_000694.2 −1.22406271 −0.14825426 2.81E−11 0.123102729 0 0.26762 1549. KIAA0240 NM_015349.1 −1.22507565 −0.24824381 1.00E−12 0.004154924 0 0.01901 1550. BCL3 NM_005178.2 −1.22811257 −0.04482055 5.66E−12 0.601406976 0 0.76062 1551. ARHGAP23 XM_290799.7 −1.2287201 0.001285621 1.57E−11 0.988672776 0 0.99512 1552. EML3 NM_153265.2 −1.22888874 −0.15256668 1.46E−12 0.066106231 0 0.1699 1553. ZNF37A NM_003421.1 −1.23034477 0.20955543 1.34E−11 0.028646756 0 0.08938 1554. ANGPT1 NM_001146.3 −1.23277337 0.222095158 3.26E−11 0.027771302 0 0.08724 1555. C5orf62 NM_032947.3 −1.23335417 −0.05705214 4.90E−12 0.505452995 0 0.68565 1556. TCEAL4 NM_001006936.1 −1.2352506 −0.34355105 8.90E−12 0.000822757 0 0.0049 1557. CHES1 NM_005197.2 −1.23542276 −0.42667702 6.19E−13 1.60E−05 0 0.00018 1558. TWIST1 NM_000474.3 −1.23546753 0.474840471 3.41E−12 1.35E−05 0 0.00016 1559. ATP2B4 NM_001001396.1 −1.24108982 −0.41928272 1.39E−11 0.000152354 0 0.00117 1560. EDN1 NM_001955.2 −1.2421427 0.553573183 2.25E−12 1.37E−06 0 2.00E−05 1561. NFE2L3 NM_004289.5 −1.24368359 1.282660919 5.03E−12 2.88E−12 0 0 1562. RIN2 NM_018993.2 −1.24377483 −0.12732257 1.26E−11 0.170097728 0 0.33581 1563. BAX NM_138765.2 −1.24393204 −0.09455657 1.82E−10 0.374229123 0 0.56948 1564. UBL4A NM_014235.3 −1.24473014 −0.05485005 2.62E−12 0.51132399 0 0.68951 1565. TMEM42 NM_144638.1 −1.24504816 −0.41076142 1.21E−12 4.35E−05 0 0.00041 1566. TAP2 NM_018833.2 −1.24679634 1.347745454 1.74E−11 4.29E−12 0 0 1567. IL18BP NM_173042.2 −1.24818958 1.396028376 5.58E−11 7.59E−12 0 0 1568. KIAA1751 NM_001080484.1 −1.24999314 0.721013137 1.17E−11 1.19E−07 0 0 1569. PDGFRB NM_002609.3 −1.25003443 −0.58162796 7.61E−12 1.93E−06 0 3.00E−05 1570. ZNF362 NM_152493.2 −1.25018261 −0.41738427 4.87E−12 9.15E−05 0 0.00076 1571. FTSJD2 NM_015050.2 −1.25058376 0.458889696 5.64E−12 3.37E−05 0 0.00033 1572. CNN2 NM_201277.1 −1.25059176 −0.62721965 5.76E−11 3.28E−06 0 5.00E−05 1573. KAT2B NM_003884.4 −1.25085462 −0.24666958 2.93E−12 0.00758648 0 0.03119 1574. PARP8 NM_024615.2 −1.25290424 0.572054226 1.04E−12 5.29E−07 0 1.00E−05 1575. DAAM2 NM_015345.2 −1.2552281 −0.05691031 1.89E−11 0.544533117 0 0.71697 1576. MAP4K2 NM_004579.2 −1.25577347 −0.24514143 2.87E−13 0.00329692 0 0.01566 1577. MTMR11 NM_181873.2 −1.25596886 0.448810783 1.48E−12 1.90E−05 0 2.00E−04 1578. BCL6 NM_001706.2 −1.25882628 0.364052652 1.15E−11 0.000653022 0 0.00403 1579. AK3 NM_016282.2 −1.25911346 −0.42562754 6.30E−13 2.11E−05 0 0.00022 1580. TTC39B NM_152574.1 −1.26035136 1.231073808 3.07E−11 4.66E−11 0 0 1581. KLF9 NM_001206.2 −1.26060289 −0.05122193 2.18E−13 0.488273883 0 0.67176 1582. COPS8 NM_006710.4 −1.26063636 0.141895302 2.56E−11 0.14816821 0 0.30536 1583. ASAM NM_024769.2 −1.26092249 0.021724338 2.37E−12 0.795291685 0 0.88975 1584. INHBE NM_031479.3 −1.26114268 −0.48724046 3.41E−10 0.00025202 0 0.00181 1585. RFTN1 NM_015150.1 −1.26124118 −0.40465466 9.94E−13 5.32E−05 0 0.00049 1586. GPX1 NM_201397.1 −1.26164419 0.316305966 1.44E−11 0.002512932 0 0.01244 1587. ANKRA2 NM_023039.2 −1.26244562 0.338540244 1.67E−12 0.000485656 0 0.00316 1588. CLDN23 NM_194284.2 −1.26399949 1.176748203 3.29E−11 1.16E−10 0 0 1589. KAT2A NM_021078.2 −1.26435612 0.060322015 2.91E−13 0.423975868 0 0.61575 1590. SLC3A2 NM_001013251.1 −1.26545795 0.646988058 2.08E−12 1.74E−07 0 0 1591. MT1G NM_005950.1 −1.26641147 0.254910746 1.51E−09 0.046262194 0 0.12953 1592. LRDD NM_018494.3 −1.26748931 0.006338396 1.29E−10 0.951967571 0 0.97732 1593. CCDC92 NM_025140.1 −1.26797415 −0.31152889 6.83E−12 0.002115927 0 0.01081 1594. MMP7 NM_002423.3 −1.2679778 0.212705137 1.56E−11 0.032117689 0 0.09767 1595. HOXA10 NM_018951.3 −1.26824789 −0.07148051 9.17E−13 0.375767851 0 0.57122 1596. LOC100129034 XM_001720357.1 −1.26934501 −0.3388464 5.08E−11 0.002680652 0 0.01312 1597. TNFAIP8 NM_001077654.1 −1.26961714 0.790314802 8.72E−12 2.81E−08 0 0 1598. NNMT NM_006169.2 −1.27135745 0.155351948 1.98E−13 0.04551244 0 0.12794 1599. TLR3 NM_003265.2 −1.27150188 1.667818088 3.74E−11 2.74E−13 0 0 1600. ABI3BP NM_015429.2 −1.27210874 −0.40694881 6.29E−13 4.11E−05 0 0.00039 1601. RNF216 NM_207111.2 −1.27291066 −0.27943523 9.26E−13 0.002160566 0 0.01099 1602. NDUFA4L2 NM_020142.3 −1.27293073 0.189521586 1.12E−10 0.082270846 0 0.2002 1603. ADARB1 NM_001112.2 −1.27392591 −0.35663003 1.62E−12 0.000312879 0 0.00217 1604. UBAP2L NM_014847.2 −1.2740099 −0.14642379 3.69E−11 0.148118985 0 0.30531 1605. GLIPR2 NM_022343.2 −1.27459398 −0.7108052 1.96E−12 4.32E−08 0 0 1606. MIR1978 NR_031742.1 −1.27530556 0.085704085 6.74E−13 0.285110377 0 0.47922 1607. MR1 NM_001531.1 −1.27624432 0.675729769 5.92E−13 3.50E−08 0 0 1608. LMO3 NM_018640.3 −1.27766577 −1.05553487 2.28E−13 7.46E−12 0 0 1609. FLJ41484 XR_042107.1 −1.28020815 −0.09400577 6.73E−13 0.244088251 0 0.4309 1610. OXTR NM_000916.3 −1.28131083 −0.80945236 2.41E−12 7.02E−09 0 0 1611. BATF2 NM_138456.3 −1.28133994 1.382835836 7.54E−12 1.90E−12 0 0 1612. CPT1A NM_001031847.1 −1.28265842 1.626021912 1.08E−12 1.32E−14 0 0 1613. YPEL3 NM_031477.4 −1.28323494 −0.2724666 5.98E−11 0.013731293 0 0.05028 1614. ALDH3A2 NM_000382.2 −1.28349337 −0.19932451 7.36E−13 0.020201185 0 0.06808 1615. SSH2 NM_033389.2 −1.28411793 −0.31835469 6.22E−12 0.001883032 0 0.0098 1616. SLC2A6 NM_017585.2 −1.28437053 0.378482079 3.37E−12 0.000279566 0 0.00197 1617. ECH1 NM_001398.2 −1.28639716 −0.34546234 2.28E−11 0.001768614 0 0.0093 1618. HSD3B7 NM_025193.2 −1.28658642 0.103366864 9.65E−12 0.270186716 0 0.46164 1619. DYRK4 NM_003845.1 −1.28717119 −0.05162009 1.31E−11 0.58398072 0 0.74633 1620. SIRT5 NM_012241.2 −1.28868154 0.21980702 5.06E−11 0.040381201 0 0.11698 1621. SIL1 NM_001037633.1 −1.29059615 −0.09340813 3.83E−10 0.416952518 0 0.60971 1622. SSBP2 NM_012446.2 −1.29355571 0.350190938 8.67E−13 0.000310366 0 0.00215 1623. SLC26A6 NM_134426.2 −1.29360831 0.136065221 2.18E−11 0.171482074 0 0.33766 1624. BCL2L13 NM_015367.2 −1.2937724 0.673244382 6.85E−12 3.57E−07 0 1.00E−05 1625. BTN3A1 NM_007048.4 −1.29603027 0.543279714 2.10E−12 3.04E−06 0 5.00E−05 1626. WDR81 NM_152348.1 −1.297512 0.005641021 1.81E−10 0.959046599 0 0.98125 1627. NRCAM NM_005010.3 −1.29976474 −0.11197225 1.30E−12 0.189586356 0 0.36299 1628. FTL NM_000146.3 −1.29977216 0.000160421 2.24E−11 0.998690037 0 0.99941 1629. AXL NM_021913.2 −1.30144788 0.099042211 6.95E−11 0.34787206 0 0.54459 1630. HTATIP2 NM_006410.3 −1.30236259 0.519560176 8.40E−12 1.58E−05 0 0.00018 1631. SUSD1 NM_022486.3 −1.30337034 0.513922476 1.21E−12 4.61E−06 0 6.00E−05 1632. CIDEC NM_022094.2 −1.30550645 −0.03097348 3.40E−12 0.726351736 0 0.84614 1633. C6orf138 NM_001013732.2 −1.30560647 0.97958877 4.10E−13 7.28E−11 0 0 1634. ZNF564 NM_144976.2 −1.30568726 −0.10146929 3.40E−13 0.202342093 0 0.3789 1635. TRIB3 NM_021158.3 −1.30713349 0.576140127 6.37E−11 1.89E−05 0 2.00E−04 1636. CENTG2 NM_014914.2 −1.30782772 0.524880457 3.72E−12 8.26E−06 0 1.00E−04 1637. KYNU NM_003937.2 −1.31136861 1.459677604 1.49E−11 2.16E−12 0 0 1638. SIX2 NM_016932.3 −1.31183369 −0.14765444 2.39E−13 0.065947869 0 0.16959 1639. EBF3 NM_001005463.1 −1.3149055 −0.55607247 1.17E−13 2.86E−07 0 1.00E−05 1640. HOXC8 NM_022658.3 −1.3151235 −0.25369686 2.67E−13 0.003504244 0 0.01648 1641. HOXC4 NM_014620.4 −1.31705844 −0.28598047 9.00E−13 0.002330636 0 0.01171 1642. SIX1 NM_005982.2 −1.31890565 0.408410823 2.44E−12 0.000137543 0 0.00107 1643. TRAM2 NM_012288.3 −1.32152945 −0.17572653 8.43E−12 0.073320888 0 0.18351 1644. KBTBD11 NM_014867.1 −1.32249933 −0.52953994 2.04E−12 5.52E−06 0 7.00E−05 1645. TMEM219 NM_001083613.1 −1.32737482 0.553093995 1.68E−13 4.76E−07 0 1.00E−05 1646. PDXK NM_003681.4 −1.32939426 −0.66103564 9.24E−13 1.35E−07 0 0 1647. FTHL2 NR_002200.1 −1.32944895 0.372503922 1.34E−09 0.007456489 0 0.03074 1648. OASL NM_003733.2 −1.3310586 1.741985948 4.39E−09 4.37E−11 0 0 1649. NEURL1B NM_001142651.1 −1.33356876 −0.32492145 3.50E−11 0.004559356 0 0.02051 1650. COMT NM_007310.1 −1.33455371 0.198907421 1.03E−11 0.049152815 0 0.13566 1651. PYCARD NM_013258.3 −1.33555746 0.423841029 2.99E−12 0.000119073 0 0.00095 1652. OSBPL5 NM_020896.2 −1.33616498 −0.066337 8.92E−12 0.489545976 0 0.67275 1653. MICAL2 NM_014632.2 −1.33709412 0.007846246 7.63E−11 0.941939083 0 0.97186 1654. ASTN2 NM_198186.2 −1.33716772 −0.22246192 1.89E−12 0.018378017 0 0.06331 1655. STAT6 NM_003153.3 −1.33735612 0.543277292 5.92E−13 1.81E−06 0 3.00E−05 1656. ST3GAL4 NM_006278.1 −1.33916714 −0.33464779 2.24E−11 0.003126343 0 0.01497 1657. ACSM5 NM_017888.2 −1.33925951 0.052274036 1.13E−11 0.590865362 0 0.75205 1658. LOC100133866 XM_001719715.1 −1.34044657 −0.13452766 2.86E−12 0.145392177 0 0.30129 1659. TGFBR3 NM_003243.2 −1.34123275 0.459930342 1.42E−13 6.27E−06 0 8.00E−05 1660. CXCL2 NM_002089.3 −1.34255656 −0.00014171 1.67E−12 0.998705957 0 0.99941 1661. IL1R1 NM_000877.2 −1.34412575 0.29854828 2.57E−12 0.003066441 0 0.01472 1662. RTN1 NM_021136.2 −1.34513809 −0.05720283 1.53E−13 0.460039047 0 0.64836 1663. MUSK NM_005592.1 −1.34833055 0.621728343 3.76E−11 7.27E−06 0 9.00E−05 1664. TANC2 NM_025185.3 −1.34885142 0.152505822 5.80E−13 0.077349509 0 0.19121 1665. A4GALT NM_017436.4 −1.34968348 0.247106452 3.48E−13 0.005691938 0 0.02459 1666. LOC644423 XM_930172.1 −1.35186033 0.002355557 1.46E−11 0.981060488 0 0.9915 1667. PTPRM NM_002845.2 −1.35229974 0.239150348 8.61E−13 0.009942472 0 0.03869 1668. LNPEP NM_175920.3 −1.35302576 2.076552667 1.06E−11 3.91E−15 0 0 1669. SCO2 NM_005138.1 −1.35315118 −0.05621753 3.13E−13 0.487127801 0 0.67073 1670. SLC7A11 NM_014331.3 −1.3550606 1.353933993 5.00E−12 5.07E−12 0 0 1671. TMBIM1 NM_022152.4 −1.35648844 0.033681867 2.75E−12 0.711009202 0 0.83581 1672. TCEAL3 NM_032926.2 −1.35654241 −0.50350419 3.01E−13 3.76E−06 0 5.00E−05 1673. TRIM47 NM_033452.2 −1.35992613 0.107549127 1.62E−12 0.232254719 0 0.41657 1674. WISP1 NM_003882.2 −1.36026694 −0.42293489 9.15E−13 7.24E−05 0 0.00063 1675. TRIM21 NM_003141.3 −1.36120539 0.978702849 5.36E−14 2.22E−11 0 0 1676. HLA-G NM_002127.3 −1.36158714 0.117153293 1.05E−12 0.185080548 0 0.35647 1677. GMPPA NM_205847.1 −1.36274104 −0.09236449 3.29E−12 0.32192772 0 0.51862 1678. SERPINE2 NM_006216.2 −1.36686711 0.204965168 3.95E−12 0.037947323 0 0.1113 1679. TLCD1 NM_138463.2 −1.36823341 −0.41257407 4.66E−12 0.000265336 0 0.00189 1680. WASF2 NM_006990.2 −1.3713366 0.172240006 6.09E−11 0.125730924 0 0.27174 1681. ABR NM_001092.3 −1.37442122 −0.08824512 6.84E−14 0.248952398 0 0.43679 1682. APCDD1L NM_153360.1 −1.37521817 0.283989552 1.92E−13 0.001768998 0 0.0093 1683. DFNA5 NM_004403.2 −1.37676256 −0.03364312 1.63E−12 0.707506944 0 0.83362 1684. PSTPIP2 NM_024430.2 −1.38071815 0.475342336 1.46E−12 2.95E−05 0 3.00E−04 1685. BIRC3 NM_182962.1 −1.38133805 0.762030268 2.66E−10 2.95E−06 0 4.00E−05 1686. SGCD NM_172244.2 −1.38361246 0.134345928 3.33E−11 0.215713603 0 0.3962 1687. EGFR NM_005228.3 −1.38570441 1.211540136 7.40E−13 8.49E−12 0 0 1688. NPTX2 NM_002523.1 −1.38607355 0.12199302 2.44E−13 0.144261408 0 0.29944 1689. DUSP10 NM_144729.1 −1.3898476 −0.36589885 3.40E−13 0.000245293 0 0.00177 1690. RELB NM_006509.2 −1.39149325 0.291381817 1.06E−13 0.001195706 0 0.00667 1691. ZNF395 NM_018660.2 −1.39214173 0.258424553 2.92E−12 0.011163004 0 0.04241 1692. ANKFY1 NM_016376.3 −1.39551572 0.094094818 1.02E−12 0.294195397 0 0.48882 1693. MCEE NM_032601.2 −1.39785582 −0.34103882 5.73E−14 0.000199452 0 0.00147 1694. CYGB NM_134268.3 −1.39837281 0.157034411 1.02E−12 0.087977277 0 0.21022 1695. SUSD2 NM_019601.3 −1.39843283 −2.02214113 6.00E−12 6.59E−15 0 0 1696. ARHGEF19 NM_153213.3 −1.40022764 0.110336957 3.26E−13 0.195395087 0 0.37013 1697. STEAP3 NM_018234.2 −1.40487084 −0.29100423 1.77E−13 0.001663157 0 0.00883 1698. RRAS NM_006270.3 −1.40541909 −0.19078881 1.10E−13 0.023869464 0 0.07777 1699. DDB2 NM_000107.1 −1.40753645 0.107266526 7.53E−13 0.230075579 0 0.41363 1700. GALK1 NM_000154.1 −1.41068025 −0.5287698 2.80E−12 1.61E−05 0 0.00018 1701. OCEL1 NM_024578.1 −1.4121561 −0.09909807 2.45E−11 0.358256689 0 0.55434 1702. C8orf13 NM_053279.1 −1.4123943 0.423496703 2.09E−13 4.36E−05 0 0.00041 1703. PLIN2 NM_001122.2 −1.41334198 0.610730944 1.28E−12 1.38E−06 0 2.00E−05 1704. PHF15 NM_015288.4 −1.41505052 0.255681623 2.00E−12 0.011596219 0 0.04373 1705. LOC653879 XM_936226.1 −1.41570984 0.326110603 5.25E−14 0.000342368 0 0.00234 1706. ZBTB4 NM_020899.2 −1.41747596 0.002479184 3.05E−14 0.97337881 0 0.98766 1707. GRINA NM_000837.1 −1.42662154 0.468347683 4.64E−12 0.00010699 0 0.00087 1708. PLA2G4C NM_003706.1 −1.42905108 0.074031317 5.43E−14 0.343549283 0 0.54053 1709. BHLHB2 NM_003670.1 −1.43040915 0.622162809 2.30E−11 1.08E−05 0 0.00013 1710. FOXQ1 NM_033260.3 −1.43194603 0.640258886 1.41E−11 5.28E−06 0 7.00E−05 1711. IMPA2 NM_014214.1 −1.43667021 −0.34113829 7.81E−13 0.001022693 0 0.00587 1712. LOC728431 XM_001132105.2 −1.44016997 0.454875198 1.74E−12 9.03E−05 0 0.00075 1713. IGFBP5 NM_000599.2 −1.4407583 0.178012333 1.93E−12 0.071191885 0 0.17968 1714. AHNAK NM_001620.1 −1.44089244 0.16302896 1.43E−11 0.133971567 0 0.28394 1715. MYH13 NM_003802.2 −1.44106374 −1.54057835 2.59E−12 7.65E−13 0 0 1716. PLXNB1 NM_002673.3 −1.44204532 −0.09842679 3.68E−12 0.321593695 0 0.51821 1717. MT2A NM_005953.2 −1.44318324 0.084693759 8.45E−14 0.295950147 0 0.49062 1718. SPTLC3 NM_018327.2 −1.44438926 0.242808954 5.24E−14 0.005053828 0 0.02229 1719. IRAK2 NM_001570.3 −1.44684212 0.511612169 1.80E−13 4.96E−06 0 7.00E−05 1720. CCDC8 NM_032040.2 −1.45318072 −0.09224991 3.24E−12 0.352429295 0 0.54879 1721. ASNS NM_133436.1 −1.4541773 0.71333254 1.05E−12 1.85E−07 0 0 1722. ATL3 NM_015459.3 −1.45534869 1.351820113 7.05E−12 2.64E−11 0 0 1723. PLEKHA4 NM_020904.1 −1.45689332 1.330489225 5.74E−13 3.01E−12 0 0 1724. PPP3CC NM_005605.3 −1.45719007 0.256236482 5.52E−14 0.003710913 0 0.01731 1725. TRIP6 NM_003302.2 −1.45738819 0.003437988 1.53E−13 0.967080994 0 0.98535 1726. LOC387763 XM_941665.2 −1.4595833 0.204766293 4.83E−14 0.015687493 0 0.05583 1727. CYP26B1 NM_019885.2 −1.46093263 0.414869119 7.55E−14 4.33E−05 0 0.00041 1728. LIMA1 NM_016357.3 −1.4628141 0.256513096 6.31E−13 0.009423844 0 0.03711 1729. AGTRAP NM_001040196.1 −1.46690619 0.615176031 1.37E−13 3.66E−07 0 1.00E−05 1730. RUSC1 NM_014328.2 −1.47032189 0.034636238 4.91E−14 0.66207751 0 0.80364 1731. P2RX6 NM_005446.3 −1.47477301 −0.74322828 1.15E−12 1.32E−07 0 0 1732. RALGDS NM_006266.2 −1.47507059 0.068597962 9.07E−13 0.463187756 0 0.65109 1733. C14orf4 NM_024496.2 −1.47638749 0.053488086 1.48E−13 0.527623056 0 0.70308 1734. PSME2 NM_002818.2 −1.47714939 0.430428021 9.35E−14 3.65E−05 0 0.00036 1735. PTPRU NM_005704.3 −1.47716192 0.26117597 6.03E−13 0.008797949 0 0.03516 1736. GBP4 NM_052941.3 −1.47784861 2.337304616 8.12E−10 2.29E−13 0 0 1737. RGS20 NM_170587.1 −1.47833808 0.086519728 8.38E−12 0.414837927 0 0.60778 1738. RRBP1 NM_001042576.1 −1.48268558 0.099040674 7.19E−13 0.289587832 0 0.48427 1739. PARP3 NM_005485.3 −1.48285466 0.160642711 6.43E−15 0.034316885 0 0.10284 1740. MIOS NM_019005.3 −1.48456566 0.123769389 1.11E−13 0.148663341 0 0.30617 1741. DNAJB2 NM_006736.5 −1.48817735 −0.01635434 1.84E−12 0.866678588 0 0.93058 1742. ABCC3 NM_003786.2 −1.49080054 0.134908152 2.08E−13 0.130736985 0 0.27892 1743. MYBPHL NM_001010985.1 −1.49245365 −0.52050028 1.51E−13 5.26E−06 0 7.00E−05 1744. CABC1 NM_020247.4 −1.49405141 −0.17570193 1.82E−12 0.083852085 0 0.20301 1745. IRAK3 NM_007199.1 −1.49963531 1.053332087 2.13E−13 1.24E−10 0 0 1746. MMP3 NM_002422.3 −1.50941637 0.283943777 3.79E−13 0.004851214 0 0.02158 1747. NFKB1 NM_003998.2 −1.5124906 0.055460651 6.37E−15 0.450306786 0 0.63957 1748. RBM43 NM_198557.2 −1.51695343 0.321509124 5.92E−12 0.006055392 0 0.0259 1749. LOC389386 XR_037483.1 −1.52070072 1.370105547 1.17E−12 7.75E−12 0 0 1750. CEBPD NM_005195.3 −1.52086996 0.159586563 1.08E−14 0.044768075 0 0.12632 1751. PDK4 NM_002612.3 −1.52095915 0.026993134 1.11E−10 0.829383614 0 0.90954 1752. DDIT4 NM_019058.2 −1.52174691 0.346018256 1.85E−13 0.000745673 0 0.00451 1753. CA9 NM_001216.1 −1.52569921 0.523674918 1.44E−13 6.27E−06 0 8.00E−05 1754. MT1A NM_005946.2 −1.52589374 −0.12115771 3.49E−13 0.193723242 0 0.36827 1755. COL8A1 NM_020351.2 −1.52684464 0.469023873 1.78E−13 2.94E−05 0 3.00E−04 1756. TRNP1 NM_001013642.2 −1.52696476 0.007844311 8.13E−14 0.925910254 0 0.9642 1757. VEZF1 NM_007146.2 −1.52847706 −0.68759888 4.95E−14 5.51E−08 0 0 1758. TRAF3IP2 NM_147686.1 −1.52911489 0.729932932 2.95E−14 1.38E−08 0 0 1759. PRKCD NM_006254.3 −1.53061669 0.34903041 1.31E−14 0.000176699 0 0.00133 1760. TCP11L1 NM_018393.2 −1.53218998 0.781612214 9.93E−14 1.35E−08 0 0 1761. SLC25A28 NM_031212.3 −1.53435397 0.725087166 2.24E−12 5.93E−07 0 1.00E−05 1762. HOXC6 NM_004503.3 −1.53945768 −0.19267894 5.83E−15 0.015807586 0 0.05619 1763. FAM175A NM_139076.2 −1.53954297 0.266657648 1.48E−12 0.013518962 0 0.04962 1764. IDH3B NM_006899.2 −1.54157745 0.071174249 2.54E−14 0.378507709 0 0.57405 1765. ZFP36L2 NM_006887.3 −1.54491503 0.733756556 1.85E−14 1.00E−08 0 0 1766. ZC3H12A NM_025079.1 −1.54576097 0.542550698 2.07E−14 1.11E−06 0 2.00E−05 1767. ISCU NM_213595.1 −1.54745085 0.039751741 9.00E−13 0.683731023 0 0.81833 1768. APOL3 NM_145641.1 −1.54756883 0.977671581 1.51E−13 5.63E−10 0 0 1769. LAP3 NM_015907.2 −1.55248459 1.401703664 7.15E−13 4.60E−12 0 0 1770. CLDN15 NM_138429.1 −1.55417589 −0.37181123 5.22E−12 0.002326424 0 0.01169 1771. PHLDA3 NM_012396.3 −1.5571977 0.195775776 5.43E−14 0.029014612 0 0.09029 1772. NT5E NM_002526.1 −1.55814764 0.488962102 4.51E−15 1.72E−06 0 3.00E−05 1773. TNS3 NM_022748.10 −1.560059 −0.16482657 1.12E−14 0.043851492 0 0.12441 1774. SLC22A18 NM_002555.3 −1.56048525 −0.05234579 8.35E−13 0.593824828 0 0.75454 1775. RCAN1 NM_203418.1 −1.56643139 0.991653906 1.01E−13 3.73E−10 0 0 1776. ESPNL NM_194312.1 −1.56733436 −0.29565305 1.05E−13 0.002820345 0 0.01374 1777. STC1 NM_003155.2 −1.57082588 0.813221894 2.70E−14 3.39E−09 0 0 1778. NFKBIZ NM_001005474.1 −1.57178323 −0.26442137 8.50E−13 0.013437646 0 0.04939 1779. ARID3A NM_005224.2 −1.57277746 0.286710916 1.34E−13 0.004049243 0 0.0186 1780. BTG2 NM_006763.2 −1.57279598 −0.12418703 6.20E−14 0.15768225 0 0.31881 1781. PRDM1 NM_001198.2 −1.5732617 −0.09376117 3.19E−13 0.322435081 0 0.51912 1782. TMEM45A NM_018004.1 −1.57441733 0.412836488 1.65E−12 0.000597758 0 0.00375 1783. FHL2 NM_201555.1 −1.58022635 −0.08794467 5.66E−14 0.310783791 0 0.50637 1784. SESN1 NM_014454.1 −1.58102515 −0.1132538 8.26E−14 0.204563372 0 0.38176 1785. SLC16A3 NM_004207.2 −1.58160744 0.487263538 4.91E−14 1.20E−05 0 0.00014 1786. MYF5 NM_005593.1 −1.58718203 0.290969968 1.14E−11 0.01861409 0 0.064 1787. TNFAIP2 NM_006291.2 −1.59343131 0.057125441 3.22E−13 0.548671707 0 0.7201 1788. PSMB10 NM_002801.2 −1.59971337 0.746410983 2.40E−13 1.16E−07 0 0 1789. CYP27A1 NM_000784.2 −1.59996322 −0.05979732 1.11E−13 0.508262417 0 0.68753 1790. FPR1 NM_002029.3 −1.60285891 0.932695249 8.65E−15 1.65E−10 0 0 1791. MSC NM_005098.3 −1.60544476 0.252937939 6.80E−14 0.008646886 0 0.03473 1792. ERAP2 NM_022350.2 −1.60546764 0.765755439 7.47E−14 3.11E−08 0 0 1793. GPX8 NM_001008397.2 −1.60600685 −0.33210501 1.14E−14 0.000443653 0 0.00291 1794. ZFP90 NM_133458.2 −1.60888346 −0.19729638 4.32E−14 0.030853859 0 0.09462 1795. GFPT2 NM_005110.1 −1.61161512 0.049446341 2.15E−14 0.552652522 0 0.72356 1796. FUCA1 NM_000147.3 −1.61457948 0.29086749 4.65E−15 0.001031226 0 0.00591 1797. ADM NM_001124.1 −1.61909121 0.636719139 5.65E−15 7.36E−08 0 0 1798. C18orf56 NM_001012716.1 −1.61938835 0.212638271 5.48E−14 0.023354241 0 0.0764 1799. BTN3A3 NM_197974.1 −1.62006729 0.401899253 1.06E−13 0.000236524 0 0.00171 1800. PDPN NM_001006625.1 −1.62289071 −0.29015177 1.44E−12 0.01108206 0 0.04217 1801. CSF3 NM_000759.2 −1.62631994 0.812630056 6.53E−15 1.73E−09 0 0 1802. KRT17 NM_000422.1 −1.62634499 0.458485309 4.13E−14 3.21E−05 0 0.00032 1803. C1RL NM_016546.1 −1.62653273 −0.15887921 1.02E−12 0.13443148 0 0.28452 1804. ID3 NM_002167.2 −1.6266375 −0.07116852 2.28E−12 0.511148191 0 0.68941 1805. NRXN2 NM_138734.1 −1.62710093 −0.24438346 1.63E−14 0.007152991 0 0.02974 1806. PTGES NM_004878.3 −1.63236485 0.31159722 8.37E−11 0.027177946 0 0.08579 1807. RBCK1 NM_031229.2 −1.63564018 0.326034854 3.82E−14 0.001137043 0 0.0064 1808. DDX60L NM_001012967.1 −1.63756912 0.657799485 2.88E−14 2.01E−07 0 0 1809. PCTK3 NM_212503.1 −1.64072889 0.593223585 3.33E−13 5.74E−06 0 8.00E−05 1810. IFIT5 NM_012420.1 −1.64540795 −0.2831098 1.18E−14 0.002318567 0 0.01167 1811. PLXNB2 NM_012401.2 −1.64908391 0.203132494 4.65E−14 0.030785988 0 0.09449 1812. HCG4 NR_002139.1 −1.65084865 0.683826828 6.23E−14 2.35E−07 0 1.00E−05 1813. MOV10 NM_020963.2 −1.65804038 0.686885229 1.41E−14 6.97E−08 0 0 1814. KLF6 NM_001008490.1 −1.65904637 0.641898836 3.14E−14 3.76E−07 0 1.00E−05 1815. RTTN NM_173630.2 −1.66298166 0.00938669 3.31E−14 0.914624753 0 0.95851 1816. SERPING1 NM_001032295.1 −1.66774893 1.213582723 1.68E−14 5.89E−12 0 0 1817. TNFRSF1A NM_001065.2 −1.67171265 0.272663339 8.11E−14 0.007323871 0 0.03031 1818. SIX5 NM_175875.3 −1.67303085 −0.36144719 7.93E−15 0.000235471 0 0.00171 1819. DCN NM_001920.3 −1.67340671 0.264127506 4.46E−15 0.003041081 0 0.01462 1820. LOC392437 XR_037197.1 −1.67432231 0.113041135 1.55E−14 0.191590462 0 0.36551 1821. FAM110B NM_147189.2 −1.67457122 −0.7651157 3.81E−14 3.46E−08 0 0 1822. TNFRSF6B NM_032945.2 −1.67781723 0.009249704 6.69E−13 0.92905655 0 0.96585 1823. HAS2 NM_005328.1 −1.67894462 0.691029466 4.16E−14 1.87E−07 0 0 1824. XBP1 NM_001079539.1 −1.67922842 0.335668137 1.50E−14 0.000706062 0 0.00431 1825. IL32 NM_001012636.1 −1.6806731 0.061122235 8.91E−15 0.461882443 0 0.64986 1826. ZNF337 NM_015655.2 −1.69290143 −0.04355874 8.45E−14 0.642972423 0 0.79019 1827. NINJ1 NM_004148.3 −1.69423643 0.210694559 8.45E−15 0.018307905 0 0.06309 1828. SQSTM1 NM_003900.3 −1.69542975 0.177118023 8.07E−15 0.042710085 0 0.12206 1829. TCEA3 NM_003196.1 −1.70592123 −0.12057791 5.05E−14 0.198902117 0 0.37451 1830. MAOA NM_000240.2 −1.7102799 −0.37585533 1.72E−13 0.000982147 0 0.00569 1831. IFITM2 NM_006435.2 −1.7127993 0.006726498 5.54E−14 0.942150711 0 0.97189 1832. MOCOS NM_017947.1 −1.71616703 0.417652421 4.47E−14 0.000177947 0 0.00134 1833. TSC22D3 NM_004089.3 −1.72924291 0.200185627 1.14E−12 0.081009325 0 0.19791 1834. GAS1 NM_002048.1 −1.73194473 0.007048827 4.70E−13 0.946577005 0 0.97406 1835. RTKN NM_033046.2 −1.73436817 −0.26783955 1.27E−13 0.012112938 0 0.04535 1836. MUC1 NM_001044390.1 −1.73973553 0.350778496 1.01E−12 0.004324357 0 0.01964 1837. RHBDF2 NM_024599.3 −1.74118145 0.381476507 4.86E−13 0.001642917 0 0.00874 1838. PPAP2B NM_177414.1 −1.74179567 0.058853912 7.93E−15 0.491185271 0 0.67383 1839. CNTNAP1 NM_003632.1 −1.74399554 0.148636651 1.49E−15 0.06775075 0 0.17309 1840. HES4 NM_021170.2 −1.75076048 1.068396514 9.76E−14 6.79E−10 0 0 1841. CRISPLD2 NM_031476.2 −1.75178737 −0.45004083 5.63E−15 2.73E−05 0 0.00028 1842. FKBP5 NM_004117.2 −1.75752416 −0.10271459 6.57E−15 0.234812689 0 0.41952 1843. CABYR NM_153768.1 −1.75759863 −0.04313195 3.71E−14 0.644015484 0 0.79107 1844. BTN3A2 NM_007047.3 −1.75860531 0.335634978 1.70E−15 0.000362323 0 0.00245 1845. VASN NM_138440.2 −1.76049327 0.287659732 5.70E−15 0.002569233 0 0.01267 1846. ZFHX3 NM_006885.3 −1.76153211 0.502851822 4.06E−15 5.76E−06 0 8.00E−05 1847. ITPRIP NM_033397.2 −1.76269453 0.551625861 4.04E−14 8.59E−06 0 0.00011 1848. SHISA5 NM_016479.3 −1.76302747 −0.27352544 6.92E−16 0.001575872 0 0.00844 1849. GSDMD NM_024736.5 −1.76317457 0.573835839 1.59E−14 2.63E−06 0 4.00E−05 1850. MSI2 NM_138962.2 −1.76336708 1.326780914 3.14E−15 6.31E−13 0 0 1851. TNFSF13B NM_006573.3 −1.76340877 2.189714333 1.09E−12 1.97E−14 0 0 1852. PCK2 NM_004563.2 −1.7757677 0.419430945 1.48E−13 0.000463907 0 0.00303 1853. C4orf18 NM_016613.4 −1.78113506 −0.51090632 2.25E−15 3.56E−06 0 5.00E−05 1854. FILIP1L NM_014890.2 −1.78355016 0.065279548 2.68E−15 0.430518135 0 0.62188 1855. NACC2 NM_144653.3 −1.78707907 0.982252798 2.29E−13 8.40E−09 0 0 1856. HLA-C NM_002117.4 −1.78750311 0.601528437 3.92E−15 5.72E−07 0 1.00E−05 1857. MLPH NM_001042467.1 −1.78774866 0.423338475 4.98E−16 1.54E−05 0 0.00017 1858. HLA-H NR_001434.1 −1.79752625 0.327002482 2.15E−13 0.004950496 0 0.02194 1859. DAB2 NM_001343.2 −1.80688296 0.10922795 2.24E−15 0.194908618 0 0.36965 1860. FST NM_013409.1 −1.81247271 0.910729653 2.67E−13 4.04E−08 0 0 1861. TMEM173 NM_198282.1 −1.81647662 0.367287652 1.95E−16 5.70E−05 0 0.00052 1862. NFIL3 NM_005384.2 −1.82334379 0.319541587 4.08E−13 0.008116955 0 0.03295 1863. ATF5 NM_012068.3 −1.82638637 0.502456405 1.13E−13 8.02E−05 0 0.00069 1864. MGC16121 XM_001128419.1 −1.82844552 0.013038775 9.76E−12 0.920850677 0 0.96188 1865. DKFZp451A211 NM_001003399.1 −1.83289652 0.308656177 5.02E−15 0.001905623 0 0.00989 1866. GALNTL2 NM_054110.3 −1.834124 0.988093636 2.27E−13 1.15E−08 0 0 1867. KIAA1618 NM_020954.2 −1.8432906 −0.2961344 3.46E−15 0.002381868 0 0.01192 1868. TAPBP NM_003190.3 −1.84402904 0.474041086 5.63E−15 2.71E−05 0 0.00028 1869. FADS1 NM_013402.3 −1.84532859 0.418638249 2.23E−15 6.64E−05 0 0.00058 1870. MAMDC2 NM_153267.3 −1.8575359 −0.02851138 1.76E−16 0.701012643 0 0.82965 1871. IHPK3 NM_054111.3 −1.85853661 −0.09088817 2.61E−15 0.294547496 0 0.48918 1872. PFKFB4 NM_004567.2 −1.86485017 0.458182595 1.37E−16 3.94E−06 0 6.00E−05 1873. SLC39A14 NM_015359.2 −1.87182882 0.480126518 5.22E−16 5.67E−06 0 8.00E−05 1874. SRGN NM_002727.2 −1.87330953 0.203053161 7.72E−16 0.019424109 0 0.06604 1875. ANGPTL2 NM_012098.2 −1.89297388 −0.7837418 1.36E−13 4.40E−07 0 1.00E−05 1876. APCDD1 NM_153000.3 −1.8940087 −0.43013755 4.23E−16 2.32E−05 0 0.00024 1877. TXNIP NM_006472.2 −1.90041037 −0.01013871 2.39E−15 0.90723328 0 0.954 1878. WARS NM_173701.1 −1.9174825 1.714743213 5.62E−14 4.46E−13 0 0 1879. HMOX1 NM_002133.1 −1.92353063 0.983827625 2.97E−14 4.51E−09 0 0 1880. RETSAT NM_017750.2 −1.92926221 −0.17305505 6.12E−15 0.073845136 0 0.18451 1881. HLA-F NM_001098479.1 −1.9323259 0.936849685 9.37E−14 2.91E−08 0 0 1882. IGFBP4 NM_001552.2 −1.93713501 0.404758921 3.54E−14 0.000716137 0 0.00436 1883. CFLAR NM_003879.3 −1.9400604 0.531255138 1.28E−14 2.13E−05 0 0.00023 1884. SEMA4B NM_198925.1 −1.94044796 0.154164008 8.14E−15 0.115409463 0 0.25581 1885. CYBASC3 NM_153611.3 −1.94506831 −0.42179468 2.75E−14 0.000441848 0 0.0029 1886. FTHL12 NR_002205.1 −1.94820294 0.387067696 1.85E−13 0.002386271 0 0.01194 1887. IFITM3 NM_021034.2 −1.94910236 −0.12744541 2.48E−16 0.118979489 0 0.26138 1888. EVC NM_014556.2 −1.95418934 −0.38572214 2.21E−14 0.000957476 0 0.00556 1889. DGKA NM_201554.1 −1.9550059 0.10137545 3.22E−15 0.272321725 0 0.46432 1890. SLC2A5 NM_003039.1 −1.95777901 0.814100831 7.46E−17 7.22E−10 0 0 1891. IRF7 NM_004029.2 −1.95885807 1.13712661 1.53E−15 3.45E−11 0 0 1892. TP53I3 NM_147184.1 −1.96051288 0.192047122 1.30E−15 0.036948411 0 0.10892 1893. UNC93B1 NM_030930.2 −1.96070175 0.941069865 1.82E−15 1.09E−09 0 0 1894. SPATA18 NM_145263.2 −1.98912505 −0.21396871 7.38E−16 0.019986924 0 0.06752 1895. CMBL NM_138809.3 −1.99166846 0.068582461 3.21E−17 0.350993311 0 0.54746 1896. CXCL6 NM_002993.2 −1.99425721 0.172815354 3.56E−12 0.210855125 0 0.39011 1897. APBB3 NM_133172.2 −1.99435525 0.039922542 1.93E−16 0.618738821 0 0.77355 1898. IFI16 NM_005531.1 −2.00849219 0.684642292 1.91E−16 4.22E−08 0 0 1899. APOBEC3G NM_021822.1 −2.01198251 1.407709172 7.16E−15 5.26E−12 0 0 1900. FTH1 NM_002032.2 −2.0286533 −0.41828197 9.42E−15 0.000413762 0 0.00275 1901. ZBTB16 NM_001018011.1 −2.03660522 0.492114038 2.55E−14 0.000139081 0 0.00108 1902. CES2 NM_003869.4 −2.04258122 0.061059702 3.02E−16 0.469468762 0 0.65591 1903. PYGB NM_002862.3 −2.0462697 −0.11799496 1.70E−16 0.158375594 0 0.31993 1904. PARP10 XM_001127571.1 −2.06434441 0.542391889 2.19E−16 2.21E−06 0 3.00E−05 1905. MT1E NM_175617.3 −2.06744305 0.128921886 5.64E−16 0.152396034 0 0.31151 1906. C14orf159 NM_024952.5 −2.06956417 0.519442851 2.48E−15 2.13E−05 0 0.00023 1907. ATOH8 NM_032827.4 −2.07341763 −0.28861999 3.95E−15 0.007189922 0 0.02986 1908. FTHL11 NR_002204.1 −2.08544399 0.60036409 5.37E−11 0.001480252 0 0.008 1909. SCHIP1 NM_014575.2 −2.09276293 0.062627023 7.81E−16 0.490657209 0 0.67346 1910. SNAI2 NM_003068.3 −2.09474629 0.202739617 5.30E−17 0.016707696 0 0.0586 1911. C20orf127 NM_080757.1 −2.097565 0.440084688 2.49E−15 0.000168115 0 0.00128 1912. PARP9 NM_031458.1 −2.09823879 0.44258682 4.51E−17 1.35E−05 0 0.00016 1913. LOC441019 XM_498969.2 −2.10656054 0.262468867 1.27E−16 0.004402357 0 0.01994 1914. ANPEP NM_001150.1 −2.1180096 0.363474839 2.43E−16 0.000376437 0 0.00254 1955. H1F0 NM_005318.2 −2.4337012 0.50036236 6.56E−18 5.13E−06 0 7.00E−05 1956. CEBPB NM_005194.2 −2.44089558 0.278291436 9.23E−18 0.003066339 0 0.01472 1957. MT1X NM_005952.2 −2.44392836 0.31620115 1.29E−16 0.003343988 0 0.01584 1958. XPC NM_004628.3 −2.45802741 0.262855334 3.54E−17 0.007993295 0 0.03257 1959. DDX58 NM_014314.3 −2.46609401 0.021135353 9.80E−17 0.824829801 0 0.90712 1960. CXCL5 NM_002994.3 −2.46876181 0.824027488 2.93E−17 1.24E−08 0 0 1961. SLC7A2 NM_001008539.2 −2.48246747 −0.10549691 4.56E−18 0.206903447 0 0.38475 1962. USP18 NM_017414.3 −2.49706957 0.995965697 3.08E−15 3.57E−08 0 0 1963. C9orf169 NM_199001.1 −2.50942513 −0.05213055 6.67E−16 0.628407413 0 0.78053 1964. TRIM25 NM_005082.4 −2.51325039 0.513858248 1.02E−18 1.48E−06 0 2.00E−05 1965. BQ437417 −2.51406874 −0.12597104 1.95E−16 0.220628257 0 0.40212 1966. CCL5 NM_002985.2 −2.52794377 1.888757888 2.25E−16 5.51E−14 0 0 1967. SAMD9L NM_152703.2 −2.53219161 1.257342146 4.23E−16 1.63E−10 0 0 1968. UBA7 NM_003335.2 −2.56074458 0.572893137 1.30E−18 4.87E−07 0 1.00E−05 1969. FTHL3 NR_002201.1 −2.57708257 0.449767394 1.95E−12 0.014144559 0 0.05134 1970. TRIM22 NM_006074.3 −2.58070903 −0.01964607 1.84E−18 0.80896617 0 0.89788 1971. PRIC285 NM_033405.2 −2.60751113 0.86339373 4.43E−16 1.31E−07 0 0 1972. AGRN NM_198576.2 −2.61234898 0.380803939 5.27E−17 0.000831554 0 0.00495 1973. CA12 NM_001218.3 −2.62949301 0.954030803 1.09E−17 1.33E−09 0 0 1974. C1Oorf10 NM_007021.2 −2.64142371 0.143168554 1.70E−16 0.18362568 0 0.35433 1975. IRF1 NM_002198.1 −2.64332853 0.356258026 1.24E−16 0.002391579 0 0.01195 1976. LOC729009 XR_042330.1 −2.65422979 0.663393857 1.60E−13 0.000274766 0 0.00194 1977. CCL2 NM_002982.3 −2.68131723 0.435521389 3.91E−17 0.000249721 0 0.00179 1978. STAT2 NM_005419.2 −2.69031186 0.18606978 7.23E−18 0.05146687 0 0.14058 1979. CHI3L2 NM_004000.2 −2.70474249 0.257337616 1.06E−15 0.040179604 0 0.11653 1980. OAS2 NM_002535.2 −2.71119798 0.455321205 6.79E−18 6.43E−05 0 0.00057 1981. TNFRSF14 NM_003820.2 −2.72030488 0.566641253 2.54E−17 1.08E−05 0 0.00013 1982. PTX3 NM_002852.2 −2.74410345 0.944168451 1.49E−15 1.93E−07 0 0 1983. HLA-B NM_005514.5 −2.75247113 0.336698468 3.15E−18 0.001076552 0 0.00612 1984. PARP14 NM_017554.1 −2.82549264 0.521139258 8.29E−16 0.000349183 0 0.00237 1985. C1R NM_001733.4 −2.82916155 0.493314318 1.56E−17 6.87E−05 0 6.00E−04 1986. DHX58 NM_024119.2 −2.83610757 0.696456542 5.70E−18 3.83E−07 0 1.00E−05 1987. SAMD9 NM_017654.2 −2.86330823 1.398759917 4.03E−16 2.07E−10 0 0 1988. TNFAIP3 NM_006290.2 −2.89673376 0.279310424 1.94E−19 0.002373549 0 0.01189 1989. STAT1 NM_007315.2 −2.91526323 0.823534962 5.93E−19 6.91E−09 0 0 1990. MT1M NM_176870.2 −2.92124936 1.185124452 2.90E−18 5.89E−11 0 0 1991. ISG20 NM_002201.4 −2.93954241 2.357383735 8.62E−16 5.49E−14 0 0 1992. SP110 NM_004510.2 −2.94061725 1.154252385 1.23E−18 4.82E−11 0 0 1993. TMEM140 NM_018295.2 −2.94612466 1.003497903 2.66E−18 1.12E−09 0 0 1994. MLKL NM_152649.1 −2.99195612 1.457088074 1.17E−18 9.49E−13 0 0 1995. NFKBIA NM_020529.1 −3.00447087 0.275123837 8.22E−19 0.006082319 0 0.026 1996. VCAM1 NM_001078.2 −3.01371818 0.634904663 9.62E−20 1.61E−07 0 0 1997. UBE2L6 NM_004223.3 −3.08486585 0.580836267 5.31E−20 5.41E−07 0 1.00E−05 1998. PSMB9 NM_002800.4 −3.13725921 0.945082183 1.75E−19 8.27E−10 0 0 1999. PARP12 NM_022750.2 −3.16502003 0.776741185 5.52E−20 9.29E−09 0 0 2000. HERC5 NM_016323.2 −3.20215105 1.329051901 5.85E−19 8.98E−12 0 0 2001. LY6E NM_002346.1 −3.25130872 0.248387222 1.22E−18 0.020878793 0 0.06983 2002. TAP1 NM_000593.5 −3.26471648 0.699574809 5.16E−20 7.58E−08 0 0 2003. VWCE NM_152718.2 −3.31730424 −0.12131841 3.29E−20 0.162954271 0 0.32605 2004. CXCL1 NM_001511.1 −3.52334103 0.202825552 4.87E−15 0.234452652 0 0.41911 2005. XAF1 NM_199139.1 −3.62201153 0.622248884 1.55E−19 4.24E−06 0 6.00E−05 2006. IFIH1 NM_022168.2 −3.70470773 1.658871536 3.25E−21 1.61E−14 0 0 2007. HERC6 NM_017912.3 −3.72816842 0.523690476 2.27E−21 3.40E−06 0 5.00E−05 2008. SLC15A3 NM_016582.1 −3.75445448 0.775468832 6.30E−20 1.56E−07 0 0 2009. C1QTNF1 NM_198594.1 −3.84595088 0.769631513 6.55E−22 6.27E−09 0 0 2010. IFI35 NM_005533.2 −3.84734525 0.916890243 1.15E−19 2.74E−08 0 0 2011. IFIT3 NM_001549.2 −3.85736134 1.806045196 4.38E−21 9.31E−15 0 0 2012. IL8 NM_000584.2 −3.88478909 1.186102426 4.85E−19 1.60E−09 0 0 2013. OAS3 NM_006187.2 −4.02902003 0.865423871 2.43E−20 3.98E−08 0 0 2014. MX2 NM_002463.1 −4.06614449 0.957591482 9.83E−20 2.91E−08 0 0 2015. LOC100129681 XM_001726834.1 −4.07488433 0.518860683 6.22E−20 9.44E−05 0 0.00078 2016. EPSTI1 NM_033255.2 −4.12032125 0.661837944 5.41E−23 2.76E−08 0 0 2017. SAA1 NM_199161.1 −4.13820981 0.256850133 9.91E−22 0.008096703 0 0.03289 2018. IFI6 NM_022872.2 −4.24031026 −0.0361139 6.20E−22 0.683302757 0 0.81802 2019. BST2 NM_004335.2 −4.24809874 0.21003593 1.36E−22 0.017358257 0 0.06038 2020. ECGF1 NM_001953.2 −4.29858283 0.615594642 2.23E−22 4.84E−07 0 1.00E−05 2021. ISG15 NM_005101.1 −4.31057423 0.127991971 3.24E−22 0.151450311 0 0.31003 2022. IFIT2 NM_001547.4 −4.31465849 2.069685191 1.68E−20 2.16E−14 0 0 2023. IFIT1 NM_001548.3 −4.37943573 0.720554258 1.96E−21 3.24E−07 0 1.00E−05 2024. OAS1 NM_001032409.1 −4.60699105 1.453177095 7.12E−20 1.68E−10 0 0 2025. SOD2 NM_001024466.1 −4.61702534 1.53216666 2.97E−22 4.31E−13 0 0 2026. IFI44L NM_006820.1 −5.11742006 0.46513265 2.83E−23 4.85E−05 0 0.00045 2027. CFB NM_001710.4 −5.6232501 0.633698868 1.91E−24 4.54E−07 0 1.00E−05 2028. MX1 NM_002462.2 −5.67457065 0.26243156 4.15E−25 0.003903492 0 0.01805 2029. IFITM1 NM_003641.3 −6.11814111 0.344079828 2.80E−24 0.001806122 0 0.00947 2030. IFI27 NM_005532.3 −6.52653374 0.274602374 1.66E−26 0.002273497 0 0.01148 *Each gene sequence in Table 1, as identified by the Genbank reference number accessed on Jul. 22, 2011, is hereby incorporated herein by reference.

While the preferred embodiment of the invention has been illustrated and described, it will be appreciated that various changes can be made therein without departing from the spirit and scope of the invention.

REFERENCES

The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference:

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1. A method of increasing or maintaining the innate immune response in a mammalian subject in need thereof, comprising administering to the mammalian subject an agent capable of inhibiting, or suppressing the level of DEFB103A and/or DEFB103B expression in a population of cells in the mammalian subject.
 2. The method of claim 1, wherein the agent specifically binds to DEFB103 polypeptide or a nucleic acid encoding DEFB103 polypeptide.
 3. The method of claim 1, wherein the agent is a DEFB103 antibody.
 4. (canceled)
 5. The method of either of claim 1, wherein the agent is a DEFB103A-specific or DEFB103B-specific siRNA.
 6. The method of claim 1, wherein the agent is capable of inhibiting DUX4-fl mediated transcriptional activation.
 7. The method of claim 1, wherein the subject in need thereof is selected from the group consisting of (i) a subject suffering from, or at risk for developing FSHD, (ii) a subject suffering from or at risk for developing myotonic dystrophy, (iii) a subject suffering from or at risk for developing Huntington's disease, (iv) a subject suffering from cancer, (v) a subject suffering from an autoimmune disease, and (vi) a subject infected with a pathogen, such as a virus, such as HIV.
 8. A method of suppressing or inhibiting the innate immune response in a mammalian subject in need thereof, comprising administering to the mammalian subject an agent capable of inducing, or increasing the level of DEFB103A and/or DEFB103B expression or activity in a population of cells in the mammalian subject. 9-17. (canceled)
 18. A method of promoting myogenesis in muscle cells comprising contacting the cells with an agent capable of inhibiting DEFB103 expression and/or DEFB103 activity. 19-25. (canceled)
 25. A method of promoting or maintaining muscle differentiation in a mammalian subject in need thereof, comprising administering to the mammalian subject an agent capable of inhibiting, or suppressing the level of DEFB103 expression and/or inhibiting DEFB103 activity in a population of muscle cells in the mammalian subject. 26-32. (canceled)
 33. A method of inhibiting the innate immune response in a mammalian subject in need thereof, comprising administering to the mammalian subject an agent capable of inducing, or increasing the level of DUX4-fl expression in a population of cells in the mammalian subject. 34-46. (canceled)
 47. A method of increasing or maintaining the innate immune response in a mammalian subject in need thereof, comprising administering to the mammalian subject an agent capable of inhibiting, or suppressing the level of DUX4-fl expression, or an agent capable of inhibiting DUX4-fl mediated transcription activation in a population of cells in the mammalian subject, wherein the mammalian subject does not suffer from, or at risk for Facioscapulohumeral Destrophy (FSHD). 48-59. (canceled)
 60. A method of inducing one or more testis expressed genes in a non-testis cell type comprising contacting the non-testis cell type with an agent capable of inducing, or increasing the level of DUX4-fl expression in a population of cells. 61-68. (canceled)
 69. A method of determining the presence of, or risk of developing, Facioscapulohumeral dystrophy (FSHD) in a mammalian subject, comprising: (a) determining the presence or amount of at least one FSHD biomarker in a biological test sample obtained from a mammalian subject, wherein the at least one FHSD biomarker comprises a gene product of a DUX-4-fl induced gene; and (b) comparing the presence or amount of the biomarker determined in step (a) with a reference standard or control sample, wherein an increase in the presence or amount of the FSHD biomarker determined in the test sample in comparison to the reference standard or control sample is indicative of the presence of FSHD, or increased risk of developing FSHD, in the mammalian subject. 70-88. (canceled)
 89. An isolated polynucleotide probe for detecting an FSHD biomarker, or a polynucleotide primer for amplifying at least a portion of an FSHD biomarker, wherein the nucleic acid probe or primer has a length of from at least 10 nucleotides to 200 nucleotides and specifically hybridizes to the nucleic acid sequence of at least two FSHD biomarker set forth in TABLE 1 or TABLE
 2. 90. An isolated population of polynucleotide probes comprising a plurality of polynucleotides each complementary and hybridizable to a sequence of at least two different FSHD biomarkers selected from any one of TABLE 1 or TABLE
 2. 91-93. (canceled)
 94. An isolated populations of antibodies that specifically bind to at least two different FSHD polypeptide biomarkers encoded by nucleic acids set forth in TABLE 1 or TABLE
 2. 95-97. (canceled)
 98. A kit comprising one or more detection reagents for detecting one or more FSHD biomarkers set forth in TABLE 1 or TABLE 2 for use in an assay to determine the presence or risk of FSHD in a biological sample obtained from a mammalian subject.
 99. A nucleic acid molecule comprising an expression cassette comprising a promoter operationally linked to a reporter gene or selectable marker, wherein the promoter contains at least one DUX4-responsive element comprising the consensus sequence “TAAYBBAATCA” (SEQ ID NO:166). 100-101. (canceled)
 102. A method of detecting the presence of DUX4-fl protein in a cell sample comprising introducing a nucleic acid molecule comprising an expression cassette comprising a promoter operationally linked to a reporter gene or selectable marker, wherein the promoter contains at least one DUX4-responsive element comprising the consensus sequence “TAAYBBAATCA” (SEQ ID NO:166), and assaying the cell for expression of the reporter gene, or selecting for growth under conditions requiring expression of the selectable marker.
 103. A method of identifying an inhibitor of DUX4-fl induced expression comprising: (a) contacting a cell containing: (i) a nucleic acid molecule comprising an expression cassette comprising a promoter operationally linked to a reporter gene or selectable marker, wherein the promoter contains at least one DUX4-responsive element comprising the consensus sequence “TAAYBBAATCA” (SEQ ID NO:166), and (ii) DUX4-fl polypeptide, with a candidate inhibitory agent; and (b) determining whether the cell expresses the reporter gene or selectable marker in the presence and absence of the candidate inhibitory agent, wherein the absence of expression of the reporter gene or selectable marker in the presence of the inhibitory agent indicates that the agent is an inhibitor of DUX4-fl induced expression. 104-105. (canceled) 